^DATABASE = GeoMiame !Database_name = Gene Expression Omnibus (GEO) !Database_institute = NCBI NLM NIH !Database_web_link = http://www.ncbi.nlm.nih.gov/geo !Database_email = geo@ncbi.nlm.nih.gov ^SERIES = GSE67835 !Series_title = A survey of human brain transcriptome diversity at the single cell level !Series_geo_accession = GSE67835 !Series_status = Public on May 20 2015 !Series_submission_date = Apr 14 2015 !Series_last_update_date = Oct 06 2017 !Series_pubmed_id = 26060301 !Series_summary = We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained from epileptic patients during temporal lobectomy for medically refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain. !Series_overall_design = Examination of cell types in healthy human brain samples. !Series_type = Expression profiling by high throughput sequencing !Series_contributor = Spyros,,Darmanis !Series_contributor = Martin,,Enge !Series_contributor = Stephen,R,Quake !Series_contributor = Steven,A,Sloan !Series_contributor = Ben,A,Barres !Series_contributor = Ye,,Zhang !Series_contributor = Christine,,Caneda !Series_contributor = Melanie,G,Hayden Gephart !Series_contributor = Lawrence,M,Shuer !Series_sample_id = GSM1657871 !Series_sample_id = GSM1657872 !Series_sample_id = GSM1657873 !Series_sample_id = GSM1657874 !Series_sample_id = GSM1657875 !Series_sample_id = GSM1657876 !Series_sample_id = GSM1657877 !Series_sample_id = GSM1657878 !Series_sample_id = GSM1657879 !Series_sample_id = GSM1657880 !Series_sample_id = GSM1657881 !Series_sample_id = GSM1657882 !Series_sample_id = GSM1657883 !Series_sample_id = GSM1657884 !Series_sample_id = GSM1657885 !Series_sample_id = GSM1657886 !Series_sample_id = GSM1657887 !Series_sample_id = GSM1657888 !Series_sample_id = GSM1657889 !Series_sample_id = GSM1657890 !Series_sample_id = GSM1657891 !Series_sample_id = GSM1657892 !Series_sample_id = GSM1657893 !Series_sample_id = GSM1657894 !Series_sample_id = GSM1657895 !Series_sample_id = GSM1657896 !Series_sample_id = GSM1657897 !Series_sample_id = GSM1657898 !Series_sample_id = GSM1657899 !Series_sample_id = GSM1657900 !Series_sample_id = GSM1657901 !Series_sample_id = GSM1657902 !Series_sample_id = GSM1657903 !Series_sample_id = GSM1657904 !Series_sample_id = GSM1657905 !Series_sample_id = GSM1657906 !Series_sample_id = GSM1657907 !Series_sample_id = GSM1657908 !Series_sample_id = GSM1657909 !Series_sample_id = GSM1657910 !Series_sample_id = GSM1657911 !Series_sample_id = GSM1657912 !Series_sample_id = GSM1657913 !Series_sample_id = GSM1657914 !Series_sample_id = GSM1657915 !Series_sample_id = GSM1657916 !Series_sample_id = GSM1657917 !Series_sample_id = GSM1657918 !Series_sample_id = GSM1657919 !Series_sample_id = GSM1657920 !Series_sample_id = GSM1657921 !Series_sample_id = GSM1657922 !Series_sample_id = GSM1657923 !Series_sample_id = GSM1657924 !Series_sample_id = GSM1657925 !Series_sample_id = GSM1657926 !Series_sample_id = GSM1657927 !Series_sample_id = GSM1657928 !Series_sample_id = GSM1657929 !Series_sample_id = GSM1657930 !Series_sample_id = GSM1657931 !Series_sample_id = GSM1657932 !Series_sample_id = GSM1657933 !Series_sample_id = GSM1657934 !Series_sample_id = GSM1657935 !Series_sample_id = GSM1657936 !Series_sample_id = GSM1657937 !Series_sample_id = GSM1657938 !Series_sample_id = GSM1657939 !Series_sample_id = GSM1657940 !Series_sample_id = GSM1657941 !Series_sample_id = GSM1657942 !Series_sample_id = GSM1657943 !Series_sample_id = GSM1657944 !Series_sample_id = GSM1657945 !Series_sample_id = GSM1657946 !Series_sample_id = GSM1657947 !Series_sample_id = GSM1657948 !Series_sample_id = GSM1657949 !Series_sample_id = GSM1657950 !Series_sample_id = GSM1657951 !Series_sample_id = GSM1657952 !Series_sample_id = GSM1657953 !Series_sample_id = GSM1657954 !Series_sample_id = GSM1657955 !Series_sample_id = GSM1657956 !Series_sample_id = GSM1657957 !Series_sample_id = GSM1657958 !Series_sample_id = GSM1657959 !Series_sample_id = GSM1657960 !Series_sample_id = GSM1657961 !Series_sample_id = GSM1657962 !Series_sample_id = GSM1657963 !Series_sample_id = GSM1657964 !Series_sample_id = GSM1657965 !Series_sample_id = GSM1657966 !Series_sample_id = GSM1657967 !Series_sample_id = GSM1657968 !Series_sample_id = GSM1657969 !Series_sample_id = GSM1657970 !Series_sample_id = GSM1657971 !Series_sample_id = GSM1657972 !Series_sample_id = GSM1657973 !Series_sample_id = GSM1657974 !Series_sample_id = GSM1657975 !Series_sample_id = GSM1657976 !Series_sample_id = GSM1657977 !Series_sample_id = GSM1657978 !Series_sample_id = GSM1657979 !Series_sample_id = GSM1657980 !Series_sample_id = GSM1657981 !Series_sample_id = GSM1657982 !Series_sample_id = GSM1657983 !Series_sample_id = GSM1657984 !Series_sample_id = GSM1657985 !Series_sample_id = GSM1657986 !Series_sample_id = GSM1657987 !Series_sample_id = GSM1657988 !Series_sample_id = GSM1657989 !Series_sample_id = GSM1657990 !Series_sample_id = GSM1657991 !Series_sample_id = GSM1657992 !Series_sample_id = GSM1657993 !Series_sample_id = GSM1657994 !Series_sample_id = GSM1657995 !Series_sample_id = GSM1657996 !Series_sample_id = GSM1657997 !Series_sample_id = GSM1657998 !Series_sample_id = GSM1657999 !Series_sample_id = GSM1658000 !Series_sample_id = GSM1658001 !Series_sample_id = GSM1658002 !Series_sample_id = GSM1658003 !Series_sample_id = GSM1658004 !Series_sample_id = GSM1658005 !Series_sample_id = GSM1658006 !Series_sample_id = GSM1658007 !Series_sample_id = GSM1658008 !Series_sample_id = GSM1658009 !Series_sample_id = GSM1658010 !Series_sample_id = GSM1658011 !Series_sample_id = GSM1658012 !Series_sample_id = GSM1658013 !Series_sample_id = GSM1658014 !Series_sample_id = GSM1658015 !Series_sample_id = GSM1658016 !Series_sample_id = GSM1658017 !Series_sample_id = GSM1658018 !Series_sample_id = GSM1658019 !Series_sample_id = GSM1658020 !Series_sample_id = GSM1658021 !Series_sample_id = GSM1658022 !Series_sample_id = GSM1658023 !Series_sample_id = GSM1658024 !Series_sample_id = GSM1658025 !Series_sample_id = GSM1658026 !Series_sample_id = GSM1658027 !Series_sample_id = GSM1658028 !Series_sample_id = GSM1658029 !Series_sample_id = GSM1658030 !Series_sample_id = GSM1658031 !Series_sample_id = GSM1658032 !Series_sample_id = GSM1658033 !Series_sample_id = GSM1658034 !Series_sample_id = GSM1658035 !Series_sample_id = GSM1658036 !Series_sample_id = GSM1658037 !Series_sample_id = GSM1658038 !Series_sample_id = GSM1658039 !Series_sample_id = GSM1658040 !Series_sample_id = GSM1658041 !Series_sample_id = GSM1658042 !Series_sample_id = GSM1658043 !Series_sample_id = GSM1658044 !Series_sample_id = GSM1658045 !Series_sample_id = GSM1658046 !Series_sample_id = GSM1658047 !Series_sample_id = GSM1658048 !Series_sample_id = GSM1658049 !Series_sample_id = GSM1658050 !Series_sample_id = GSM1658051 !Series_sample_id = GSM1658052 !Series_sample_id = GSM1658053 !Series_sample_id = GSM1658054 !Series_sample_id = GSM1658055 !Series_sample_id = GSM1658056 !Series_sample_id = GSM1658057 !Series_sample_id = GSM1658058 !Series_sample_id = GSM1658059 !Series_sample_id = GSM1658060 !Series_sample_id = GSM1658061 !Series_sample_id = GSM1658062 !Series_sample_id = GSM1658063 !Series_sample_id = GSM1658064 !Series_sample_id = GSM1658065 !Series_sample_id = GSM1658066 !Series_sample_id = GSM1658067 !Series_sample_id = GSM1658068 !Series_sample_id = GSM1658069 !Series_sample_id = GSM1658070 !Series_sample_id = GSM1658071 !Series_sample_id = GSM1658072 !Series_sample_id = GSM1658073 !Series_sample_id = GSM1658074 !Series_sample_id = GSM1658075 !Series_sample_id = GSM1658076 !Series_sample_id = GSM1658077 !Series_sample_id = GSM1658078 !Series_sample_id = GSM1658079 !Series_sample_id = GSM1658080 !Series_sample_id = GSM1658081 !Series_sample_id = GSM1658082 !Series_sample_id = GSM1658083 !Series_sample_id = GSM1658084 !Series_sample_id = GSM1658085 !Series_sample_id = GSM1658086 !Series_sample_id = GSM1658087 !Series_sample_id = GSM1658088 !Series_sample_id = GSM1658089 !Series_sample_id = GSM1658090 !Series_sample_id = GSM1658091 !Series_sample_id = GSM1658092 !Series_sample_id = GSM1658093 !Series_sample_id = GSM1658094 !Series_sample_id = GSM1658095 !Series_sample_id = GSM1658096 !Series_sample_id = GSM1658097 !Series_sample_id = GSM1658098 !Series_sample_id = GSM1658099 !Series_sample_id = GSM1658100 !Series_sample_id = GSM1658101 !Series_sample_id = GSM1658102 !Series_sample_id = GSM1658103 !Series_sample_id = GSM1658104 !Series_sample_id = GSM1658105 !Series_sample_id = GSM1658106 !Series_sample_id = GSM1658107 !Series_sample_id = GSM1658108 !Series_sample_id = GSM1658109 !Series_sample_id = GSM1658110 !Series_sample_id = GSM1658111 !Series_sample_id = GSM1658112 !Series_sample_id = GSM1658113 !Series_sample_id = GSM1658114 !Series_sample_id = GSM1658115 !Series_sample_id = GSM1658116 !Series_sample_id = GSM1658117 !Series_sample_id = GSM1658118 !Series_sample_id = GSM1658119 !Series_sample_id = GSM1658120 !Series_sample_id = GSM1658121 !Series_sample_id = GSM1658122 !Series_sample_id = GSM1658123 !Series_sample_id = GSM1658124 !Series_sample_id = GSM1658125 !Series_sample_id = GSM1658126 !Series_sample_id = GSM1658127 !Series_sample_id = GSM1658128 !Series_sample_id = GSM1658129 !Series_sample_id = GSM1658130 !Series_sample_id = GSM1658131 !Series_sample_id = GSM1658132 !Series_sample_id = GSM1658133 !Series_sample_id = GSM1658134 !Series_sample_id = GSM1658135 !Series_sample_id = GSM1658136 !Series_sample_id = GSM1658137 !Series_sample_id = GSM1658138 !Series_sample_id = GSM1658139 !Series_sample_id = GSM1658140 !Series_sample_id = GSM1658141 !Series_sample_id = GSM1658142 !Series_sample_id = GSM1658143 !Series_sample_id = GSM1658144 !Series_sample_id = GSM1658145 !Series_sample_id = GSM1658146 !Series_sample_id = GSM1658147 !Series_sample_id = GSM1658148 !Series_sample_id = GSM1658149 !Series_sample_id = GSM1658150 !Series_sample_id = GSM1658151 !Series_sample_id = GSM1658152 !Series_sample_id = GSM1658153 !Series_sample_id = GSM1658154 !Series_sample_id = GSM1658155 !Series_sample_id = GSM1658156 !Series_sample_id = GSM1658157 !Series_sample_id = GSM1658158 !Series_sample_id = GSM1658159 !Series_sample_id = GSM1658160 !Series_sample_id = GSM1658161 !Series_sample_id = GSM1658162 !Series_sample_id = GSM1658163 !Series_sample_id = GSM1658164 !Series_sample_id = GSM1658165 !Series_sample_id = GSM1658166 !Series_sample_id = GSM1658167 !Series_sample_id = GSM1658168 !Series_sample_id = GSM1658169 !Series_sample_id = GSM1658170 !Series_sample_id = GSM1658171 !Series_sample_id = GSM1658172 !Series_sample_id = GSM1658173 !Series_sample_id = GSM1658174 !Series_sample_id = GSM1658175 !Series_sample_id = GSM1658176 !Series_sample_id = GSM1658177 !Series_sample_id = GSM1658178 !Series_sample_id = GSM1658179 !Series_sample_id = GSM1658180 !Series_sample_id = GSM1658181 !Series_sample_id = GSM1658182 !Series_sample_id = GSM1658183 !Series_sample_id = GSM1658184 !Series_sample_id = GSM1658185 !Series_sample_id = GSM1658186 !Series_sample_id = GSM1658187 !Series_sample_id = GSM1658188 !Series_sample_id = GSM1658189 !Series_sample_id = GSM1658190 !Series_sample_id = GSM1658191 !Series_sample_id = GSM1658192 !Series_sample_id = GSM1658193 !Series_sample_id = GSM1658194 !Series_sample_id = GSM1658195 !Series_sample_id = GSM1658196 !Series_sample_id = GSM1658197 !Series_sample_id = GSM1658198 !Series_sample_id = GSM1658199 !Series_sample_id = GSM1658200 !Series_sample_id = GSM1658201 !Series_sample_id = GSM1658202 !Series_sample_id = GSM1658203 !Series_sample_id = GSM1658204 !Series_sample_id = GSM1658205 !Series_sample_id = GSM1658206 !Series_sample_id = GSM1658207 !Series_sample_id = GSM1658208 !Series_sample_id = GSM1658209 !Series_sample_id = GSM1658210 !Series_sample_id = GSM1658211 !Series_sample_id = GSM1658212 !Series_sample_id = GSM1658213 !Series_sample_id = GSM1658214 !Series_sample_id = GSM1658215 !Series_sample_id = GSM1658216 !Series_sample_id = GSM1658217 !Series_sample_id = GSM1658218 !Series_sample_id = GSM1658219 !Series_sample_id = GSM1658220 !Series_sample_id = GSM1658221 !Series_sample_id = GSM1658222 !Series_sample_id = GSM1658223 !Series_sample_id = GSM1658224 !Series_sample_id = GSM1658225 !Series_sample_id = GSM1658226 !Series_sample_id = GSM1658227 !Series_sample_id = GSM1658228 !Series_sample_id = GSM1658229 !Series_sample_id = GSM1658230 !Series_sample_id = GSM1658231 !Series_sample_id = GSM1658232 !Series_sample_id = GSM1658233 !Series_sample_id = GSM1658234 !Series_sample_id = GSM1658235 !Series_sample_id = GSM1658236 !Series_sample_id = GSM1658237 !Series_sample_id = GSM1658238 !Series_sample_id = GSM1658239 !Series_sample_id = GSM1658240 !Series_sample_id = GSM1658241 !Series_sample_id = GSM1658242 !Series_sample_id = GSM1658243 !Series_sample_id = GSM1658244 !Series_sample_id = GSM1658245 !Series_sample_id = GSM1658246 !Series_sample_id = GSM1658247 !Series_sample_id = GSM1658248 !Series_sample_id = GSM1658249 !Series_sample_id = GSM1658251 !Series_sample_id = GSM1658253 !Series_sample_id = GSM1658255 !Series_sample_id = GSM1658257 !Series_sample_id = GSM1658259 !Series_sample_id = GSM1658262 !Series_sample_id = GSM1658264 !Series_sample_id = GSM1658266 !Series_sample_id = GSM1658268 !Series_sample_id = GSM1658270 !Series_sample_id = GSM1658272 !Series_sample_id = GSM1658275 !Series_sample_id = GSM1658277 !Series_sample_id = GSM1658279 !Series_sample_id = GSM1658281 !Series_sample_id = GSM1658284 !Series_sample_id = GSM1658286 !Series_sample_id = GSM1658288 !Series_sample_id = GSM1658290 !Series_sample_id = GSM1658292 !Series_sample_id = GSM1658294 !Series_sample_id = GSM1658297 !Series_sample_id = GSM1658299 !Series_sample_id = GSM1658301 !Series_sample_id = GSM1658304 !Series_sample_id = GSM1658305 !Series_sample_id = GSM1658306 !Series_sample_id = GSM1658307 !Series_sample_id = GSM1658308 !Series_sample_id = GSM1658309 !Series_sample_id = GSM1658310 !Series_sample_id = GSM1658311 !Series_sample_id = GSM1658312 !Series_sample_id = GSM1658313 !Series_sample_id = GSM1658314 !Series_sample_id = GSM1658315 !Series_sample_id = GSM1658316 !Series_sample_id = GSM1658317 !Series_sample_id = GSM1658318 !Series_sample_id = GSM1658319 !Series_sample_id = GSM1658320 !Series_sample_id = GSM1658321 !Series_sample_id = GSM1658322 !Series_sample_id = GSM1658323 !Series_sample_id = GSM1658324 !Series_sample_id = GSM1658325 !Series_sample_id = GSM1658326 !Series_sample_id = GSM1658327 !Series_sample_id = GSM1658328 !Series_sample_id = GSM1658329 !Series_sample_id = GSM1658330 !Series_sample_id = GSM1658331 !Series_sample_id = GSM1658332 !Series_sample_id = GSM1658333 !Series_sample_id = GSM1658334 !Series_sample_id = GSM1658335 !Series_sample_id = GSM1658336 !Series_sample_id = GSM1658337 !Series_sample_id = GSM1658338 !Series_sample_id = GSM1658339 !Series_sample_id = GSM1658340 !Series_sample_id = GSM1658341 !Series_sample_id = GSM1658342 !Series_sample_id = GSM1658343 !Series_sample_id = GSM1658344 !Series_sample_id = GSM1658345 !Series_sample_id = GSM1658346 !Series_sample_id = GSM1658347 !Series_sample_id = GSM1658348 !Series_sample_id = GSM1658349 !Series_sample_id = GSM1658350 !Series_sample_id = GSM1658351 !Series_sample_id = GSM1658352 !Series_sample_id = GSM1658353 !Series_sample_id = GSM1658354 !Series_sample_id = GSM1658355 !Series_sample_id = GSM1658356 !Series_sample_id = GSM1658357 !Series_sample_id = GSM1658358 !Series_sample_id = GSM1658359 !Series_sample_id = GSM1658360 !Series_sample_id = GSM1658361 !Series_sample_id = GSM1658362 !Series_sample_id = GSM1658363 !Series_sample_id = GSM1658364 !Series_sample_id = GSM1658365 !Series_sample_id = GSM1658366 !Series_contact_name = Martin,,Enge !Series_contact_email = martin.enge@ki.se !Series_contact_department = Dep of Oncology-Pathology !Series_contact_institute = Karolinska Institute !Series_contact_address = CCK, Z4 !Series_contact_city = Stockholm !Series_contact_zip/postal_code = S-171 76 !Series_contact_country = Sweden !Series_supplementary_file = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP057/SRP057196 !Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67835/suppl/GSE67835_RAW.tar !Series_platform_id = GPL15520 !Series_platform_id = GPL18573 !Series_platform_taxid = 9606 !Series_sample_taxid = 9606 !Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA281204 !Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP057196 ^PLATFORM = GPL15520 !Platform_title = Illumina MiSeq (Homo sapiens) !Platform_geo_accession = GPL15520 !Platform_status = Public on May 02 2012 !Platform_submission_date = May 02 2012 !Platform_last_update_date = Sep 14 2017 !Platform_technology = high-throughput sequencing !Platform_distribution = virtual !Platform_organism = Homo sapiens !Platform_taxid = 9606 !Platform_contact_name = ,,GEO !Platform_contact_country = USA !Platform_data_row_count = 0 ^PLATFORM = GPL18573 !Platform_title = Illumina NextSeq 500 (Homo sapiens) !Platform_geo_accession = GPL18573 !Platform_status = Public on Apr 15 2014 !Platform_submission_date = Apr 15 2014 !Platform_last_update_date = Oct 06 2017 !Platform_technology = high-throughput sequencing !Platform_distribution = virtual !Platform_organism = Homo sapiens !Platform_taxid = 9606 !Platform_contact_name = ,,GEO !Platform_contact_country = USA !Platform_data_row_count = 0 ^SAMPLE = GSM1657871 !Sample_title = healthy cortex cell 1 !Sample_geo_accession = GSM1657871 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486326 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995861 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657871/suppl/GSM1657871_1772078217.C03.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995861 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657872 !Sample_title = healthy cortex cell 2 !Sample_geo_accession = GSM1657872 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486327 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995862 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657872/suppl/GSM1657872_1772078217.C04.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995862 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657873 !Sample_title = healthy cortex cell 3 !Sample_geo_accession = GSM1657873 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486328 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995863 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657873/suppl/GSM1657873_1772078217.C06.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995863 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657874 !Sample_title = healthy cortex cell 4 !Sample_geo_accession = GSM1657874 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486329 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995864 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657874/suppl/GSM1657874_1772078217.C07.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995864 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657875 !Sample_title = healthy cortex cell 5 !Sample_geo_accession = GSM1657875 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486330 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995865 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657875/suppl/GSM1657875_1772078217.C08.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995865 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657876 !Sample_title = healthy cortex cell 6 !Sample_geo_accession = GSM1657876 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486331 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995866 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657876/suppl/GSM1657876_1772078217.C09.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995866 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657877 !Sample_title = healthy cortex cell 7 !Sample_geo_accession = GSM1657877 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486332 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995867 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657877/suppl/GSM1657877_1772078217.C14.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995867 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657878 !Sample_title = healthy cortex cell 8 !Sample_geo_accession = GSM1657878 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486333 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995868 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657878/suppl/GSM1657878_1772078217.C16.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995868 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657879 !Sample_title = healthy cortex cell 9 !Sample_geo_accession = GSM1657879 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486334 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995869 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657879/suppl/GSM1657879_1772078217.C17.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995869 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657880 !Sample_title = healthy cortex cell 10 !Sample_geo_accession = GSM1657880 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486335 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995870 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657880/suppl/GSM1657880_1772078217.C18.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995870 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657881 !Sample_title = healthy cortex cell 11 !Sample_geo_accession = GSM1657881 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486336 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995871 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657881/suppl/GSM1657881_1772078217.C20.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995871 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657882 !Sample_title = healthy cortex cell 12 !Sample_geo_accession = GSM1657882 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486337 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995872 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657882/suppl/GSM1657882_1772078217.C23.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995872 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657883 !Sample_title = healthy cortex cell 13 !Sample_geo_accession = GSM1657883 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486338 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995873 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657883/suppl/GSM1657883_1772078217.C28.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995873 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657884 !Sample_title = healthy cortex cell 14 !Sample_geo_accession = GSM1657884 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486339 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995874 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657884/suppl/GSM1657884_1772078217.C29.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995874 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657885 !Sample_title = healthy cortex cell 15 !Sample_geo_accession = GSM1657885 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486340 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995875 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657885/suppl/GSM1657885_1772078217.C32.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995875 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657886 !Sample_title = healthy cortex cell 16 !Sample_geo_accession = GSM1657886 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486341 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995876 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657886/suppl/GSM1657886_1772078217.C33.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995876 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657887 !Sample_title = healthy cortex cell 17 !Sample_geo_accession = GSM1657887 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486342 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995877 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657887/suppl/GSM1657887_1772078217.C39.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995877 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657888 !Sample_title = healthy cortex cell 18 !Sample_geo_accession = GSM1657888 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486343 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995878 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657888/suppl/GSM1657888_1772078217.C40.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995878 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657889 !Sample_title = healthy cortex cell 19 !Sample_geo_accession = GSM1657889 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486344 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995879 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657889/suppl/GSM1657889_1772078217.C47.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995879 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657890 !Sample_title = healthy cortex cell 20 !Sample_geo_accession = GSM1657890 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486358 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995880 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657890/suppl/GSM1657890_1772078217.C52.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995880 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657891 !Sample_title = healthy cortex cell 21 !Sample_geo_accession = GSM1657891 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486355 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995881 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657891/suppl/GSM1657891_1772078217.C56.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995881 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657892 !Sample_title = healthy cortex cell 22 !Sample_geo_accession = GSM1657892 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486356 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995882 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657892/suppl/GSM1657892_1772078217.C58.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995882 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657893 !Sample_title = healthy cortex cell 23 !Sample_geo_accession = GSM1657893 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486357 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995883 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657893/suppl/GSM1657893_1772078217.C59.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995883 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657894 !Sample_title = healthy cortex cell 24 !Sample_geo_accession = GSM1657894 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486345 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995884 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657894/suppl/GSM1657894_1772078217.C60.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995884 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657895 !Sample_title = healthy cortex cell 25 !Sample_geo_accession = GSM1657895 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486346 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995885 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657895/suppl/GSM1657895_1772078217.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995885 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657896 !Sample_title = healthy cortex cell 26 !Sample_geo_accession = GSM1657896 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486347 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995886 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657896/suppl/GSM1657896_1772078217.C66.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995886 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657897 !Sample_title = healthy cortex cell 27 !Sample_geo_accession = GSM1657897 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486348 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995887 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657897/suppl/GSM1657897_1772078217.C72.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995887 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657898 !Sample_title = healthy cortex cell 28 !Sample_geo_accession = GSM1657898 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486349 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995888 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657898/suppl/GSM1657898_1772078217.C80.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995888 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657899 !Sample_title = healthy cortex cell 29 !Sample_geo_accession = GSM1657899 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486350 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995889 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657899/suppl/GSM1657899_1772078217.C87.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995889 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657900 !Sample_title = healthy cortex cell 30 !Sample_geo_accession = GSM1657900 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486351 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995890 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657900/suppl/GSM1657900_1772078217.C89.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995890 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657901 !Sample_title = healthy cortex cell 31 !Sample_geo_accession = GSM1657901 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486352 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995891 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657901/suppl/GSM1657901_1772078217.C91.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995891 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657902 !Sample_title = healthy cortex cell 32 !Sample_geo_accession = GSM1657902 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486353 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995892 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657902/suppl/GSM1657902_1772078217.C94.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995892 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657903 !Sample_title = healthy cortex cell 33 !Sample_geo_accession = GSM1657903 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078217 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486296 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995893 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657903/suppl/GSM1657903_1772078217.C96.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995893 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657904 !Sample_title = healthy cortex cell 34 !Sample_geo_accession = GSM1657904 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486297 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995894 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657904/suppl/GSM1657904_1772078218.C05.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995894 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657905 !Sample_title = healthy cortex cell 35 !Sample_geo_accession = GSM1657905 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486298 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995895 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657905/suppl/GSM1657905_1772078218.C08.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995895 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657906 !Sample_title = healthy cortex cell 36 !Sample_geo_accession = GSM1657906 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486299 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995896 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657906/suppl/GSM1657906_1772078218.C09.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995896 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657907 !Sample_title = healthy cortex cell 37 !Sample_geo_accession = GSM1657907 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486300 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995897 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657907/suppl/GSM1657907_1772078218.C13.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995897 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657908 !Sample_title = healthy cortex cell 38 !Sample_geo_accession = GSM1657908 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486301 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995898 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657908/suppl/GSM1657908_1772078218.C18.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995898 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657909 !Sample_title = healthy cortex cell 39 !Sample_geo_accession = GSM1657909 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486302 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995899 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657909/suppl/GSM1657909_1772078218.C23.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995899 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657910 !Sample_title = healthy cortex cell 40 !Sample_geo_accession = GSM1657910 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486303 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995900 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657910/suppl/GSM1657910_1772078218.C27.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995900 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657911 !Sample_title = healthy cortex cell 41 !Sample_geo_accession = GSM1657911 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486304 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995901 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657911/suppl/GSM1657911_1772078218.C29.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995901 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657912 !Sample_title = healthy cortex cell 42 !Sample_geo_accession = GSM1657912 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486305 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995902 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657912/suppl/GSM1657912_1772078218.C32.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995902 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657913 !Sample_title = healthy cortex cell 43 !Sample_geo_accession = GSM1657913 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486306 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995903 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657913/suppl/GSM1657913_1772078218.C34.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995903 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657914 !Sample_title = healthy cortex cell 44 !Sample_geo_accession = GSM1657914 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486307 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995904 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657914/suppl/GSM1657914_1772078218.C43.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995904 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657915 !Sample_title = healthy cortex cell 45 !Sample_geo_accession = GSM1657915 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486308 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995905 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657915/suppl/GSM1657915_1772078218.C44.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995905 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657916 !Sample_title = healthy cortex cell 46 !Sample_geo_accession = GSM1657916 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486309 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995906 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657916/suppl/GSM1657916_1772078218.C47.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995906 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657917 !Sample_title = healthy cortex cell 47 !Sample_geo_accession = GSM1657917 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486310 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995907 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657917/suppl/GSM1657917_1772078218.C48.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995907 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657918 !Sample_title = healthy cortex cell 48 !Sample_geo_accession = GSM1657918 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486311 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995908 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657918/suppl/GSM1657918_1772078218.C53.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995908 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657919 !Sample_title = healthy cortex cell 49 !Sample_geo_accession = GSM1657919 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486312 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995909 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657919/suppl/GSM1657919_1772078218.C55.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995909 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657920 !Sample_title = healthy cortex cell 50 !Sample_geo_accession = GSM1657920 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486313 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995910 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657920/suppl/GSM1657920_1772078218.C56.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995910 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657921 !Sample_title = healthy cortex cell 51 !Sample_geo_accession = GSM1657921 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486314 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995911 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657921/suppl/GSM1657921_1772078218.C58.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995911 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657922 !Sample_title = healthy cortex cell 52 !Sample_geo_accession = GSM1657922 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486315 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995912 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657922/suppl/GSM1657922_1772078218.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995912 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657923 !Sample_title = healthy cortex cell 53 !Sample_geo_accession = GSM1657923 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486316 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995913 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657923/suppl/GSM1657923_1772078218.C71.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995913 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657924 !Sample_title = healthy cortex cell 54 !Sample_geo_accession = GSM1657924 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486317 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995914 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657924/suppl/GSM1657924_1772078218.C85.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995914 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657925 !Sample_title = healthy cortex cell 55 !Sample_geo_accession = GSM1657925 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486318 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995915 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657925/suppl/GSM1657925_1772078218.C88.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995915 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657926 !Sample_title = healthy cortex cell 56 !Sample_geo_accession = GSM1657926 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486319 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995916 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657926/suppl/GSM1657926_1772078218.C89.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995916 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657927 !Sample_title = healthy cortex cell 57 !Sample_geo_accession = GSM1657927 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486320 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995917 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657927/suppl/GSM1657927_1772078218.C93.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995917 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657928 !Sample_title = healthy cortex cell 58 !Sample_geo_accession = GSM1657928 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: OPC !Sample_characteristics_ch1 = age: postnatal 54 years !Sample_characteristics_ch1 = c1 chip id: 1772078218 !Sample_characteristics_ch1 = experiment_sample_name: AB_S8 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486321 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995918 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657928/suppl/GSM1657928_1772078218.C95.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995918 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657929 !Sample_title = healthy cortex cell 59 !Sample_geo_accession = GSM1657929 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486322 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995919 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657929/suppl/GSM1657929_1772078236.C11.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995919 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657930 !Sample_title = healthy cortex cell 60 !Sample_geo_accession = GSM1657930 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486323 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995920 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657930/suppl/GSM1657930_1772078236.C12.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995920 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657931 !Sample_title = healthy cortex cell 61 !Sample_geo_accession = GSM1657931 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486324 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995921 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657931/suppl/GSM1657931_1772078236.C16.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995921 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657932 !Sample_title = healthy cortex cell 62 !Sample_geo_accession = GSM1657932 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486325 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995922 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657932/suppl/GSM1657932_1772078236.C17.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995922 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657933 !Sample_title = healthy cortex cell 63 !Sample_geo_accession = GSM1657933 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486359 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995923 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657933/suppl/GSM1657933_1772078236.C19.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995923 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657934 !Sample_title = healthy cortex cell 64 !Sample_geo_accession = GSM1657934 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486354 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995924 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657934/suppl/GSM1657934_1772078236.C25.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995924 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657935 !Sample_title = healthy cortex cell 65 !Sample_geo_accession = GSM1657935 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486266 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995925 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657935/suppl/GSM1657935_1772078236.C26.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995925 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657936 !Sample_title = healthy cortex cell 66 !Sample_geo_accession = GSM1657936 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486267 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995926 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657936/suppl/GSM1657936_1772078236.C27.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995926 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657937 !Sample_title = healthy cortex cell 67 !Sample_geo_accession = GSM1657937 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486268 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995927 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657937/suppl/GSM1657937_1772078236.C28.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995927 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657938 !Sample_title = healthy cortex cell 68 !Sample_geo_accession = GSM1657938 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486269 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995928 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657938/suppl/GSM1657938_1772078236.C30.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995928 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657939 !Sample_title = healthy cortex cell 69 !Sample_geo_accession = GSM1657939 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486270 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995929 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657939/suppl/GSM1657939_1772078236.C31.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995929 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657940 !Sample_title = healthy cortex cell 70 !Sample_geo_accession = GSM1657940 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486271 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995930 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657940/suppl/GSM1657940_1772078236.C32.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995930 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657941 !Sample_title = healthy cortex cell 71 !Sample_geo_accession = GSM1657941 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486272 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995931 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657941/suppl/GSM1657941_1772078236.C33.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995931 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657942 !Sample_title = healthy cortex cell 72 !Sample_geo_accession = GSM1657942 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486273 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995932 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657942/suppl/GSM1657942_1772078236.C34.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995932 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657943 !Sample_title = healthy cortex cell 73 !Sample_geo_accession = GSM1657943 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486274 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995933 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657943/suppl/GSM1657943_1772078236.C36.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995933 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657944 !Sample_title = healthy cortex cell 74 !Sample_geo_accession = GSM1657944 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486275 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995934 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657944/suppl/GSM1657944_1772078236.C38.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995934 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657945 !Sample_title = healthy cortex cell 75 !Sample_geo_accession = GSM1657945 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486276 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995935 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657945/suppl/GSM1657945_1772078236.C40.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995935 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657946 !Sample_title = healthy cortex cell 76 !Sample_geo_accession = GSM1657946 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486277 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995936 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657946/suppl/GSM1657946_1772078236.C41.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995936 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657947 !Sample_title = healthy cortex cell 77 !Sample_geo_accession = GSM1657947 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486278 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995937 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657947/suppl/GSM1657947_1772078236.C45.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995937 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657948 !Sample_title = healthy cortex cell 78 !Sample_geo_accession = GSM1657948 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486279 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995938 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657948/suppl/GSM1657948_1772078236.C46.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995938 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657949 !Sample_title = healthy cortex cell 79 !Sample_geo_accession = GSM1657949 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486280 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995939 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657949/suppl/GSM1657949_1772078236.C47.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995939 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657950 !Sample_title = healthy cortex cell 80 !Sample_geo_accession = GSM1657950 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486281 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995940 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657950/suppl/GSM1657950_1772078236.C49.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995940 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657951 !Sample_title = healthy cortex cell 81 !Sample_geo_accession = GSM1657951 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486282 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995941 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657951/suppl/GSM1657951_1772078236.C54.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995941 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657952 !Sample_title = healthy cortex cell 82 !Sample_geo_accession = GSM1657952 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486283 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995942 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657952/suppl/GSM1657952_1772078236.C56.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995942 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657953 !Sample_title = healthy cortex cell 83 !Sample_geo_accession = GSM1657953 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486284 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995943 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657953/suppl/GSM1657953_1772078236.C57.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995943 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657954 !Sample_title = healthy cortex cell 84 !Sample_geo_accession = GSM1657954 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486285 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995944 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657954/suppl/GSM1657954_1772078236.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995944 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657955 !Sample_title = healthy cortex cell 85 !Sample_geo_accession = GSM1657955 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486286 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995945 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657955/suppl/GSM1657955_1772078236.C65.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995945 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657956 !Sample_title = healthy cortex cell 86 !Sample_geo_accession = GSM1657956 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486287 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995946 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657956/suppl/GSM1657956_1772078236.C66.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995946 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657957 !Sample_title = healthy cortex cell 87 !Sample_geo_accession = GSM1657957 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486288 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995947 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657957/suppl/GSM1657957_1772078236.C70.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995947 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657958 !Sample_title = healthy cortex cell 88 !Sample_geo_accession = GSM1657958 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486289 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995948 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657958/suppl/GSM1657958_1772078236.C74.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995948 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657959 !Sample_title = healthy cortex cell 89 !Sample_geo_accession = GSM1657959 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486290 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995949 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657959/suppl/GSM1657959_1772078236.C77.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995949 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657960 !Sample_title = healthy cortex cell 90 !Sample_geo_accession = GSM1657960 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486291 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995950 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657960/suppl/GSM1657960_1772078236.C89.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995950 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657961 !Sample_title = healthy cortex cell 91 !Sample_geo_accession = GSM1657961 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486292 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995951 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657961/suppl/GSM1657961_1772078236.C90.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995951 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657962 !Sample_title = healthy cortex cell 92 !Sample_geo_accession = GSM1657962 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078236 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486293 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995952 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657962/suppl/GSM1657962_1772078236.C93.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995952 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657963 !Sample_title = healthy cortex cell 93 !Sample_geo_accession = GSM1657963 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486294 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995953 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657963/suppl/GSM1657963_1772078237.C06.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995953 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657964 !Sample_title = healthy cortex cell 94 !Sample_geo_accession = GSM1657964 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486295 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995954 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657964/suppl/GSM1657964_1772078237.C08.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995954 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657965 !Sample_title = healthy cortex cell 95 !Sample_geo_accession = GSM1657965 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486236 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995955 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657965/suppl/GSM1657965_1772078237.C11.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995955 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657966 !Sample_title = healthy cortex cell 96 !Sample_geo_accession = GSM1657966 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486237 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995956 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657966/suppl/GSM1657966_1772078237.C13.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995956 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657967 !Sample_title = healthy cortex cell 97 !Sample_geo_accession = GSM1657967 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486238 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995957 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657967/suppl/GSM1657967_1772078237.C14.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995957 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657968 !Sample_title = healthy cortex cell 98 !Sample_geo_accession = GSM1657968 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486239 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995958 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657968/suppl/GSM1657968_1772078237.C15.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995958 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657969 !Sample_title = healthy cortex cell 99 !Sample_geo_accession = GSM1657969 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486240 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995959 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657969/suppl/GSM1657969_1772078237.C19.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995959 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657970 !Sample_title = healthy cortex cell 100 !Sample_geo_accession = GSM1657970 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486241 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995960 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657970/suppl/GSM1657970_1772078237.C21.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995960 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657971 !Sample_title = healthy cortex cell 101 !Sample_geo_accession = GSM1657971 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486242 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995961 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657971/suppl/GSM1657971_1772078237.C26.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995961 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657972 !Sample_title = healthy cortex cell 102 !Sample_geo_accession = GSM1657972 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486243 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995962 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657972/suppl/GSM1657972_1772078237.C28.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995962 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657973 !Sample_title = healthy cortex cell 103 !Sample_geo_accession = GSM1657973 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486244 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995963 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657973/suppl/GSM1657973_1772078237.C29.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995963 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657974 !Sample_title = healthy cortex cell 104 !Sample_geo_accession = GSM1657974 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486245 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995964 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657974/suppl/GSM1657974_1772078237.C31.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995964 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657975 !Sample_title = healthy cortex cell 105 !Sample_geo_accession = GSM1657975 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486246 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995965 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657975/suppl/GSM1657975_1772078237.C40.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995965 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657976 !Sample_title = healthy cortex cell 106 !Sample_geo_accession = GSM1657976 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486247 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995966 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657976/suppl/GSM1657976_1772078237.C42.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995966 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657977 !Sample_title = healthy cortex cell 107 !Sample_geo_accession = GSM1657977 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486248 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995967 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657977/suppl/GSM1657977_1772078237.C44.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995967 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657978 !Sample_title = healthy cortex cell 108 !Sample_geo_accession = GSM1657978 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486249 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995968 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657978/suppl/GSM1657978_1772078237.C47.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995968 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657979 !Sample_title = healthy cortex cell 109 !Sample_geo_accession = GSM1657979 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486250 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995969 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657979/suppl/GSM1657979_1772078237.C49.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995969 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657980 !Sample_title = healthy cortex cell 110 !Sample_geo_accession = GSM1657980 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486251 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995970 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657980/suppl/GSM1657980_1772078237.C52.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995970 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657981 !Sample_title = healthy cortex cell 111 !Sample_geo_accession = GSM1657981 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486252 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995971 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657981/suppl/GSM1657981_1772078237.C55.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995971 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657982 !Sample_title = healthy cortex cell 112 !Sample_geo_accession = GSM1657982 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486253 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995972 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657982/suppl/GSM1657982_1772078237.C56.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995972 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657983 !Sample_title = healthy cortex cell 113 !Sample_geo_accession = GSM1657983 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486254 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995973 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657983/suppl/GSM1657983_1772078237.C58.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995973 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657984 !Sample_title = healthy cortex cell 114 !Sample_geo_accession = GSM1657984 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486255 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995974 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657984/suppl/GSM1657984_1772078237.C60.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995974 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657985 !Sample_title = healthy cortex cell 115 !Sample_geo_accession = GSM1657985 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486256 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995975 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657985/suppl/GSM1657985_1772078237.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995975 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657986 !Sample_title = healthy cortex cell 116 !Sample_geo_accession = GSM1657986 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486257 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995976 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657986/suppl/GSM1657986_1772078237.C62.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995976 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657987 !Sample_title = healthy cortex cell 117 !Sample_geo_accession = GSM1657987 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486258 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995977 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657987/suppl/GSM1657987_1772078237.C74.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995977 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657988 !Sample_title = healthy cortex cell 118 !Sample_geo_accession = GSM1657988 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486259 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995978 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657988/suppl/GSM1657988_1772078237.C79.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995978 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657989 !Sample_title = healthy cortex cell 119 !Sample_geo_accession = GSM1657989 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486260 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995979 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657989/suppl/GSM1657989_1772078237.C83.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995979 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657990 !Sample_title = healthy cortex cell 120 !Sample_geo_accession = GSM1657990 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486261 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995980 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657990/suppl/GSM1657990_1772078237.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995980 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657991 !Sample_title = healthy cortex cell 121 !Sample_geo_accession = GSM1657991 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 37 years !Sample_characteristics_ch1 = c1 chip id: 1772078237 !Sample_characteristics_ch1 = experiment_sample_name: AB_S11 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486262 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995981 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657991/suppl/GSM1657991_1772078237.C92.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995981 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657992 !Sample_title = healthy cortex cell 122 !Sample_geo_accession = GSM1657992 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID12 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486263 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995982 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657992/suppl/GSM1657992_nochipID12.C05.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995982 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657993 !Sample_title = healthy cortex cell 123 !Sample_geo_accession = GSM1657993 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID12 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486264 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995983 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657993/suppl/GSM1657993_nochipID12.C23.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995983 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657994 !Sample_title = healthy cortex cell 124 !Sample_geo_accession = GSM1657994 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID12 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486265 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995984 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657994/suppl/GSM1657994_nochipID12.C73.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995984 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657995 !Sample_title = healthy cortex cell 125 !Sample_geo_accession = GSM1657995 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID12 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486206 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995985 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657995/suppl/GSM1657995_nochipID12.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995985 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657996 !Sample_title = healthy cortex cell 126 !Sample_geo_accession = GSM1657996 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID12 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486207 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995986 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657996/suppl/GSM1657996_nochipID12.C87.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995986 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657997 !Sample_title = healthy cortex cell 127 !Sample_geo_accession = GSM1657997 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID14 !Sample_characteristics_ch1 = experiment_sample_name: AB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486208 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995987 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657997/suppl/GSM1657997_nochipID14.C08.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995987 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657998 !Sample_title = healthy cortex cell 128 !Sample_geo_accession = GSM1657998 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID14 !Sample_characteristics_ch1 = experiment_sample_name: AB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486209 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995988 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657998/suppl/GSM1657998_nochipID14.C13.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995988 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1657999 !Sample_title = healthy cortex cell 129 !Sample_geo_accession = GSM1657999 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID14 !Sample_characteristics_ch1 = experiment_sample_name: AB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486210 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995989 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657999/suppl/GSM1657999_nochipID14.C29.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995989 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658000 !Sample_title = healthy cortex cell 130 !Sample_geo_accession = GSM1658000 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID14 !Sample_characteristics_ch1 = experiment_sample_name: AB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486211 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995990 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658000/suppl/GSM1658000_nochipID14.C45.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995990 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658001 !Sample_title = healthy cortex cell 131 !Sample_geo_accession = GSM1658001 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID14 !Sample_characteristics_ch1 = experiment_sample_name: AB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486212 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995991 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658001/suppl/GSM1658001_nochipID14.C89.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995991 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658002 !Sample_title = healthy cortex cell 132 !Sample_geo_accession = GSM1658002 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 22 years !Sample_characteristics_ch1 = c1 chip id: nochipID15 !Sample_characteristics_ch1 = experiment_sample_name: AB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486213 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995992 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658002/suppl/GSM1658002_nochipID15.C20.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995992 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658003 !Sample_title = healthy cortex cell 133 !Sample_geo_accession = GSM1658003 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: postnatal 22 years !Sample_characteristics_ch1 = c1 chip id: nochipID15 !Sample_characteristics_ch1 = experiment_sample_name: AB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486214 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995993 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658003/suppl/GSM1658003_nochipID15.C54.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995993 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658004 !Sample_title = healthy cortex cell 134 !Sample_geo_accession = GSM1658004 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 22 years !Sample_characteristics_ch1 = c1 chip id: nochipID15 !Sample_characteristics_ch1 = experiment_sample_name: AB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486215 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995994 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658004/suppl/GSM1658004_nochipID15.C69.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995994 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658005 !Sample_title = healthy cortex cell 135 !Sample_geo_accession = GSM1658005 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 22 years !Sample_characteristics_ch1 = c1 chip id: nochipID15 !Sample_characteristics_ch1 = experiment_sample_name: AB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486216 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995995 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658005/suppl/GSM1658005_nochipID15.C86.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995995 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658006 !Sample_title = healthy cortex cell 136 !Sample_geo_accession = GSM1658006 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486217 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995996 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658006/suppl/GSM1658006_nochipID2.C01.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995996 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658007 !Sample_title = healthy cortex cell 137 !Sample_geo_accession = GSM1658007 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486218 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995997 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658007/suppl/GSM1658007_nochipID2.C02.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995997 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658008 !Sample_title = healthy cortex cell 138 !Sample_geo_accession = GSM1658008 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486219 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995998 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658008/suppl/GSM1658008_nochipID2.C03.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995998 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658009 !Sample_title = healthy cortex cell 139 !Sample_geo_accession = GSM1658009 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486220 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX995999 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658009/suppl/GSM1658009_nochipID2.C07.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995999 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658010 !Sample_title = healthy cortex cell 140 !Sample_geo_accession = GSM1658010 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486221 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996000 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658010/suppl/GSM1658010_nochipID2.C08.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996000 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658011 !Sample_title = healthy cortex cell 141 !Sample_geo_accession = GSM1658011 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486222 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996001 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658011/suppl/GSM1658011_nochipID2.C09.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996001 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658012 !Sample_title = healthy cortex cell 142 !Sample_geo_accession = GSM1658012 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486223 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996002 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658012/suppl/GSM1658012_nochipID2.C10.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996002 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658013 !Sample_title = healthy cortex cell 143 !Sample_geo_accession = GSM1658013 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486224 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996003 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658013/suppl/GSM1658013_nochipID2.C11.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996003 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658014 !Sample_title = healthy cortex cell 144 !Sample_geo_accession = GSM1658014 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486225 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996004 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658014/suppl/GSM1658014_nochipID2.C12.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996004 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658015 !Sample_title = healthy cortex cell 145 !Sample_geo_accession = GSM1658015 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486226 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996005 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658015/suppl/GSM1658015_nochipID2.C13.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996005 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658016 !Sample_title = healthy cortex cell 146 !Sample_geo_accession = GSM1658016 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486227 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996006 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658016/suppl/GSM1658016_nochipID2.C14.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996006 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658017 !Sample_title = healthy cortex cell 147 !Sample_geo_accession = GSM1658017 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486228 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996007 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658017/suppl/GSM1658017_nochipID2.C15.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996007 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658018 !Sample_title = healthy cortex cell 148 !Sample_geo_accession = GSM1658018 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486229 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996008 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658018/suppl/GSM1658018_nochipID2.C16.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996008 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658019 !Sample_title = healthy cortex cell 149 !Sample_geo_accession = GSM1658019 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486230 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996009 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658019/suppl/GSM1658019_nochipID2.C17.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996009 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658020 !Sample_title = healthy cortex cell 150 !Sample_geo_accession = GSM1658020 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486231 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996010 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658020/suppl/GSM1658020_nochipID2.C18.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996010 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658021 !Sample_title = healthy cortex cell 151 !Sample_geo_accession = GSM1658021 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486232 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996011 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658021/suppl/GSM1658021_nochipID2.C19.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996011 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658022 !Sample_title = healthy cortex cell 152 !Sample_geo_accession = GSM1658022 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486233 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996012 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658022/suppl/GSM1658022_nochipID2.C21.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996012 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658023 !Sample_title = healthy cortex cell 153 !Sample_geo_accession = GSM1658023 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486234 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996013 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658023/suppl/GSM1658023_nochipID2.C22.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996013 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658024 !Sample_title = healthy cortex cell 154 !Sample_geo_accession = GSM1658024 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486235 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996014 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658024/suppl/GSM1658024_nochipID2.C24.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996014 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658025 !Sample_title = healthy cortex cell 155 !Sample_geo_accession = GSM1658025 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486176 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996015 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658025/suppl/GSM1658025_nochipID2.C26.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996015 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658026 !Sample_title = healthy cortex cell 156 !Sample_geo_accession = GSM1658026 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486177 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996016 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658026/suppl/GSM1658026_nochipID2.C27.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996016 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658027 !Sample_title = healthy cortex cell 157 !Sample_geo_accession = GSM1658027 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486178 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996017 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658027/suppl/GSM1658027_nochipID2.C28.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996017 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658028 !Sample_title = healthy cortex cell 158 !Sample_geo_accession = GSM1658028 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486179 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996018 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658028/suppl/GSM1658028_nochipID2.C29.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996018 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658029 !Sample_title = healthy cortex cell 159 !Sample_geo_accession = GSM1658029 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486180 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996019 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658029/suppl/GSM1658029_nochipID2.C30.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996019 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658030 !Sample_title = healthy cortex cell 160 !Sample_geo_accession = GSM1658030 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486181 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996020 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658030/suppl/GSM1658030_nochipID2.C31.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996020 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658031 !Sample_title = healthy cortex cell 161 !Sample_geo_accession = GSM1658031 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486182 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996021 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658031/suppl/GSM1658031_nochipID2.C32.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996021 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658032 !Sample_title = healthy cortex cell 162 !Sample_geo_accession = GSM1658032 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486183 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996022 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658032/suppl/GSM1658032_nochipID2.C33.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996022 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658033 !Sample_title = healthy cortex cell 163 !Sample_geo_accession = GSM1658033 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486184 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996023 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658033/suppl/GSM1658033_nochipID2.C34.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996023 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658034 !Sample_title = healthy cortex cell 164 !Sample_geo_accession = GSM1658034 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486185 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996024 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658034/suppl/GSM1658034_nochipID2.C36.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996024 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658035 !Sample_title = healthy cortex cell 165 !Sample_geo_accession = GSM1658035 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486186 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996025 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658035/suppl/GSM1658035_nochipID2.C38.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996025 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658036 !Sample_title = healthy cortex cell 166 !Sample_geo_accession = GSM1658036 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486187 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996026 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658036/suppl/GSM1658036_nochipID2.C39.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996026 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658037 !Sample_title = healthy cortex cell 167 !Sample_geo_accession = GSM1658037 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486188 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996027 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658037/suppl/GSM1658037_nochipID2.C40.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996027 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658038 !Sample_title = healthy cortex cell 168 !Sample_geo_accession = GSM1658038 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486189 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996028 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658038/suppl/GSM1658038_nochipID2.C41.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996028 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658039 !Sample_title = healthy cortex cell 169 !Sample_geo_accession = GSM1658039 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486190 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996029 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658039/suppl/GSM1658039_nochipID2.C42.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996029 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658040 !Sample_title = healthy cortex cell 170 !Sample_geo_accession = GSM1658040 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486191 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996030 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658040/suppl/GSM1658040_nochipID2.C43.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996030 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658041 !Sample_title = healthy cortex cell 171 !Sample_geo_accession = GSM1658041 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486192 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996031 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658041/suppl/GSM1658041_nochipID2.C44.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996031 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658042 !Sample_title = healthy cortex cell 172 !Sample_geo_accession = GSM1658042 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486193 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996032 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658042/suppl/GSM1658042_nochipID2.C45.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996032 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658043 !Sample_title = healthy cortex cell 173 !Sample_geo_accession = GSM1658043 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486194 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996033 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658043/suppl/GSM1658043_nochipID2.C46.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996033 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658044 !Sample_title = healthy cortex cell 174 !Sample_geo_accession = GSM1658044 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486195 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996034 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658044/suppl/GSM1658044_nochipID2.C47.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996034 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658045 !Sample_title = healthy cortex cell 175 !Sample_geo_accession = GSM1658045 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486196 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996035 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658045/suppl/GSM1658045_nochipID2.C48.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996035 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658046 !Sample_title = healthy cortex cell 176 !Sample_geo_accession = GSM1658046 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486197 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996036 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658046/suppl/GSM1658046_nochipID2.C49.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996036 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658047 !Sample_title = healthy cortex cell 177 !Sample_geo_accession = GSM1658047 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486198 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996037 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658047/suppl/GSM1658047_nochipID2.C50.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996037 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658048 !Sample_title = healthy cortex cell 178 !Sample_geo_accession = GSM1658048 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486199 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996038 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658048/suppl/GSM1658048_nochipID2.C51.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996038 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658049 !Sample_title = healthy cortex cell 179 !Sample_geo_accession = GSM1658049 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486200 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996039 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658049/suppl/GSM1658049_nochipID2.C52.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996039 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658050 !Sample_title = healthy cortex cell 180 !Sample_geo_accession = GSM1658050 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486201 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996040 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658050/suppl/GSM1658050_nochipID2.C56.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996040 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658051 !Sample_title = healthy cortex cell 181 !Sample_geo_accession = GSM1658051 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486202 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996041 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658051/suppl/GSM1658051_nochipID2.C57.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996041 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658052 !Sample_title = healthy cortex cell 182 !Sample_geo_accession = GSM1658052 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486203 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996042 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658052/suppl/GSM1658052_nochipID2.C58.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996042 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658053 !Sample_title = healthy cortex cell 183 !Sample_geo_accession = GSM1658053 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486204 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996043 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658053/suppl/GSM1658053_nochipID2.C59.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996043 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658054 !Sample_title = healthy cortex cell 184 !Sample_geo_accession = GSM1658054 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486205 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996044 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658054/suppl/GSM1658054_nochipID2.C60.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996044 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658055 !Sample_title = healthy cortex cell 185 !Sample_geo_accession = GSM1658055 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486146 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996045 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658055/suppl/GSM1658055_nochipID2.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996045 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658056 !Sample_title = healthy cortex cell 186 !Sample_geo_accession = GSM1658056 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486147 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996046 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658056/suppl/GSM1658056_nochipID2.C62.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996046 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658057 !Sample_title = healthy cortex cell 187 !Sample_geo_accession = GSM1658057 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486148 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996047 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658057/suppl/GSM1658057_nochipID2.C63.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996047 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658058 !Sample_title = healthy cortex cell 188 !Sample_geo_accession = GSM1658058 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486149 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996048 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658058/suppl/GSM1658058_nochipID2.C64.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996048 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658059 !Sample_title = healthy cortex cell 189 !Sample_geo_accession = GSM1658059 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486150 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996049 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658059/suppl/GSM1658059_nochipID2.C65.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996049 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658060 !Sample_title = healthy cortex cell 190 !Sample_geo_accession = GSM1658060 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486151 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996050 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658060/suppl/GSM1658060_nochipID2.C66.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996050 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658061 !Sample_title = healthy cortex cell 191 !Sample_geo_accession = GSM1658061 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486152 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996051 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658061/suppl/GSM1658061_nochipID2.C67.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996051 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658062 !Sample_title = healthy cortex cell 192 !Sample_geo_accession = GSM1658062 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486153 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996052 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658062/suppl/GSM1658062_nochipID2.C68.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996052 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658063 !Sample_title = healthy cortex cell 193 !Sample_geo_accession = GSM1658063 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486154 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996053 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658063/suppl/GSM1658063_nochipID2.C69.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996053 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658064 !Sample_title = healthy cortex cell 194 !Sample_geo_accession = GSM1658064 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486155 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996054 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658064/suppl/GSM1658064_nochipID2.C71.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996054 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658065 !Sample_title = healthy cortex cell 195 !Sample_geo_accession = GSM1658065 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486156 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996055 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658065/suppl/GSM1658065_nochipID2.C73.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996055 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658066 !Sample_title = healthy cortex cell 196 !Sample_geo_accession = GSM1658066 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486157 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996056 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658066/suppl/GSM1658066_nochipID2.C75.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996056 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658067 !Sample_title = healthy cortex cell 197 !Sample_geo_accession = GSM1658067 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486158 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996057 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658067/suppl/GSM1658067_nochipID2.C76.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996057 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658068 !Sample_title = healthy cortex cell 198 !Sample_geo_accession = GSM1658068 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486159 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996058 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658068/suppl/GSM1658068_nochipID2.C77.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996058 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658069 !Sample_title = healthy cortex cell 199 !Sample_geo_accession = GSM1658069 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486160 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996059 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658069/suppl/GSM1658069_nochipID2.C78.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996059 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658070 !Sample_title = healthy cortex cell 200 !Sample_geo_accession = GSM1658070 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486161 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996060 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658070/suppl/GSM1658070_nochipID2.C79.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996060 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658071 !Sample_title = healthy cortex cell 201 !Sample_geo_accession = GSM1658071 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486162 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996061 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658071/suppl/GSM1658071_nochipID2.C80.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996061 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658072 !Sample_title = healthy cortex cell 202 !Sample_geo_accession = GSM1658072 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486163 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996062 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658072/suppl/GSM1658072_nochipID2.C81.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996062 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658073 !Sample_title = healthy cortex cell 203 !Sample_geo_accession = GSM1658073 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486164 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996063 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658073/suppl/GSM1658073_nochipID2.C82.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996063 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658074 !Sample_title = healthy cortex cell 204 !Sample_geo_accession = GSM1658074 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486165 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996064 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658074/suppl/GSM1658074_nochipID2.C83.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996064 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658075 !Sample_title = healthy cortex cell 205 !Sample_geo_accession = GSM1658075 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486168 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996065 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658075/suppl/GSM1658075_nochipID2.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996065 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658076 !Sample_title = healthy cortex cell 206 !Sample_geo_accession = GSM1658076 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486169 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996066 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658076/suppl/GSM1658076_nochipID2.C85.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996066 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658077 !Sample_title = healthy cortex cell 207 !Sample_geo_accession = GSM1658077 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486170 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996067 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658077/suppl/GSM1658077_nochipID2.C86.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996067 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658078 !Sample_title = healthy cortex cell 208 !Sample_geo_accession = GSM1658078 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486171 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996068 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658078/suppl/GSM1658078_nochipID2.C87.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996068 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658079 !Sample_title = healthy cortex cell 209 !Sample_geo_accession = GSM1658079 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486172 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996069 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658079/suppl/GSM1658079_nochipID2.C89.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996069 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658080 !Sample_title = healthy cortex cell 210 !Sample_geo_accession = GSM1658080 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486173 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996070 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658080/suppl/GSM1658080_nochipID2.C90.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996070 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658081 !Sample_title = healthy cortex cell 211 !Sample_geo_accession = GSM1658081 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486166 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996071 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658081/suppl/GSM1658081_nochipID2.C92.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996071 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658082 !Sample_title = healthy cortex cell 212 !Sample_geo_accession = GSM1658082 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 50 years !Sample_characteristics_ch1 = c1 chip id: nochipID2 !Sample_characteristics_ch1 = experiment_sample_name: AB_S4 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486167 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996072 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658082/suppl/GSM1658082_nochipID2.C93.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996072 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658083 !Sample_title = healthy cortex cell 213 !Sample_geo_accession = GSM1658083 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486174 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996073 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658083/suppl/GSM1658083_nochipID3.C01.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996073 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658084 !Sample_title = healthy cortex cell 214 !Sample_geo_accession = GSM1658084 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486175 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996074 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658084/suppl/GSM1658084_nochipID3.C05.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996074 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658085 !Sample_title = healthy cortex cell 215 !Sample_geo_accession = GSM1658085 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486116 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996075 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658085/suppl/GSM1658085_nochipID3.C06.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996075 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658086 !Sample_title = healthy cortex cell 216 !Sample_geo_accession = GSM1658086 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486117 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996076 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658086/suppl/GSM1658086_nochipID3.C07.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996076 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658087 !Sample_title = healthy cortex cell 217 !Sample_geo_accession = GSM1658087 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486118 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996077 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658087/suppl/GSM1658087_nochipID3.C09.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996077 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658088 !Sample_title = healthy cortex cell 218 !Sample_geo_accession = GSM1658088 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486119 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996078 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658088/suppl/GSM1658088_nochipID3.C11.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996078 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658089 !Sample_title = healthy cortex cell 219 !Sample_geo_accession = GSM1658089 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486120 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996079 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658089/suppl/GSM1658089_nochipID3.C12.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996079 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658090 !Sample_title = healthy cortex cell 220 !Sample_geo_accession = GSM1658090 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486121 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996080 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658090/suppl/GSM1658090_nochipID3.C14.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996080 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658091 !Sample_title = healthy cortex cell 221 !Sample_geo_accession = GSM1658091 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486122 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996081 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658091/suppl/GSM1658091_nochipID3.C23.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996081 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658092 !Sample_title = healthy cortex cell 222 !Sample_geo_accession = GSM1658092 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486123 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996082 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658092/suppl/GSM1658092_nochipID3.C25.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996082 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658093 !Sample_title = healthy cortex cell 223 !Sample_geo_accession = GSM1658093 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486124 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996083 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658093/suppl/GSM1658093_nochipID3.C32.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996083 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658094 !Sample_title = healthy cortex cell 224 !Sample_geo_accession = GSM1658094 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486125 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996084 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658094/suppl/GSM1658094_nochipID3.C37.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996084 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658095 !Sample_title = healthy cortex cell 225 !Sample_geo_accession = GSM1658095 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486126 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996085 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658095/suppl/GSM1658095_nochipID3.C38.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996085 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658096 !Sample_title = healthy cortex cell 226 !Sample_geo_accession = GSM1658096 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486127 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996086 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658096/suppl/GSM1658096_nochipID3.C51.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996086 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658097 !Sample_title = healthy cortex cell 227 !Sample_geo_accession = GSM1658097 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486128 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996087 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658097/suppl/GSM1658097_nochipID3.C52.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996087 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658098 !Sample_title = healthy cortex cell 228 !Sample_geo_accession = GSM1658098 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486129 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996088 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658098/suppl/GSM1658098_nochipID3.C53.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996088 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658099 !Sample_title = healthy cortex cell 229 !Sample_geo_accession = GSM1658099 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486130 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996089 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658099/suppl/GSM1658099_nochipID3.C54.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996089 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658100 !Sample_title = healthy cortex cell 230 !Sample_geo_accession = GSM1658100 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486131 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996090 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658100/suppl/GSM1658100_nochipID3.C56.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996090 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658101 !Sample_title = healthy cortex cell 231 !Sample_geo_accession = GSM1658101 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486132 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996091 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658101/suppl/GSM1658101_nochipID3.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996091 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658102 !Sample_title = healthy cortex cell 232 !Sample_geo_accession = GSM1658102 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486133 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996092 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658102/suppl/GSM1658102_nochipID3.C62.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996092 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658103 !Sample_title = healthy cortex cell 233 !Sample_geo_accession = GSM1658103 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486134 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996093 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658103/suppl/GSM1658103_nochipID3.C65.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996093 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658104 !Sample_title = healthy cortex cell 234 !Sample_geo_accession = GSM1658104 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486135 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996094 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658104/suppl/GSM1658104_nochipID3.C69.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996094 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658105 !Sample_title = healthy cortex cell 235 !Sample_geo_accession = GSM1658105 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486136 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996095 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658105/suppl/GSM1658105_nochipID3.C71.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996095 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658106 !Sample_title = healthy cortex cell 236 !Sample_geo_accession = GSM1658106 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486137 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996096 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658106/suppl/GSM1658106_nochipID3.C72.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996096 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658107 !Sample_title = healthy cortex cell 237 !Sample_geo_accession = GSM1658107 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486138 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996097 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658107/suppl/GSM1658107_nochipID3.C74.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996097 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658108 !Sample_title = healthy cortex cell 238 !Sample_geo_accession = GSM1658108 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486139 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996098 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658108/suppl/GSM1658108_nochipID3.C75.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996098 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658109 !Sample_title = healthy cortex cell 239 !Sample_geo_accession = GSM1658109 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486140 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996099 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658109/suppl/GSM1658109_nochipID3.C76.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996099 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658110 !Sample_title = healthy cortex cell 240 !Sample_geo_accession = GSM1658110 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486141 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996100 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658110/suppl/GSM1658110_nochipID3.C80.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996100 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658111 !Sample_title = healthy cortex cell 241 !Sample_geo_accession = GSM1658111 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486142 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996101 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658111/suppl/GSM1658111_nochipID3.C81.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996101 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658112 !Sample_title = healthy cortex cell 242 !Sample_geo_accession = GSM1658112 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486143 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996102 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658112/suppl/GSM1658112_nochipID3.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996102 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658113 !Sample_title = healthy cortex cell 243 !Sample_geo_accession = GSM1658113 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486144 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996103 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658113/suppl/GSM1658113_nochipID3.C85.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996103 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658114 !Sample_title = healthy cortex cell 244 !Sample_geo_accession = GSM1658114 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486145 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996104 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658114/suppl/GSM1658114_nochipID3.C86.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996104 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658115 !Sample_title = healthy cortex cell 245 !Sample_geo_accession = GSM1658115 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID3 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486086 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996105 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658115/suppl/GSM1658115_nochipID3.C91.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996105 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658116 !Sample_title = healthy cortex cell 246 !Sample_geo_accession = GSM1658116 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486087 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996106 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658116/suppl/GSM1658116_nochipID5.C04.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996106 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658117 !Sample_title = healthy cortex cell 247 !Sample_geo_accession = GSM1658117 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486088 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996107 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658117/suppl/GSM1658117_nochipID5.C05.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996107 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658118 !Sample_title = healthy cortex cell 248 !Sample_geo_accession = GSM1658118 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486089 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996108 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658118/suppl/GSM1658118_nochipID5.C18.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996108 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658119 !Sample_title = healthy cortex cell 249 !Sample_geo_accession = GSM1658119 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486090 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996109 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658119/suppl/GSM1658119_nochipID5.C19.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996109 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658120 !Sample_title = healthy cortex cell 250 !Sample_geo_accession = GSM1658120 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486091 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996110 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658120/suppl/GSM1658120_nochipID5.C42.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996110 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658121 !Sample_title = healthy cortex cell 251 !Sample_geo_accession = GSM1658121 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486092 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996111 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658121/suppl/GSM1658121_nochipID5.C44.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996111 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658122 !Sample_title = healthy cortex cell 252 !Sample_geo_accession = GSM1658122 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486093 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996112 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658122/suppl/GSM1658122_nochipID5.C45.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996112 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658123 !Sample_title = healthy cortex cell 253 !Sample_geo_accession = GSM1658123 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486094 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996113 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658123/suppl/GSM1658123_nochipID5.C54.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996113 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658124 !Sample_title = healthy cortex cell 254 !Sample_geo_accession = GSM1658124 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486095 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996114 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658124/suppl/GSM1658124_nochipID5.C65.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996114 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658125 !Sample_title = healthy cortex cell 255 !Sample_geo_accession = GSM1658125 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486096 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996115 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658125/suppl/GSM1658125_nochipID5.C72.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996115 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658126 !Sample_title = healthy cortex cell 256 !Sample_geo_accession = GSM1658126 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: hippocampus !Sample_characteristics_ch1 = cell type: endothelial !Sample_characteristics_ch1 = age: postnatal 63 years !Sample_characteristics_ch1 = c1 chip id: nochipID5 !Sample_characteristics_ch1 = experiment_sample_name: AB_S5 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486097 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996116 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658126/suppl/GSM1658126_nochipID5.C91.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996116 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658127 !Sample_title = healthy cortex cell 257 !Sample_geo_accession = GSM1658127 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486098 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996117 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658127/suppl/GSM1658127_nochipID8.C01.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996117 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658128 !Sample_title = healthy cortex cell 258 !Sample_geo_accession = GSM1658128 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486099 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996118 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658128/suppl/GSM1658128_nochipID8.C02.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996118 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658129 !Sample_title = healthy cortex cell 259 !Sample_geo_accession = GSM1658129 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486100 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996119 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658129/suppl/GSM1658129_nochipID8.C05.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996119 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658130 !Sample_title = healthy cortex cell 260 !Sample_geo_accession = GSM1658130 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486101 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996120 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658130/suppl/GSM1658130_nochipID8.C06.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996120 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658131 !Sample_title = healthy cortex cell 261 !Sample_geo_accession = GSM1658131 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486102 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996121 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658131/suppl/GSM1658131_nochipID8.C08.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996121 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658132 !Sample_title = healthy cortex cell 262 !Sample_geo_accession = GSM1658132 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486103 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996122 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658132/suppl/GSM1658132_nochipID8.C11.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996122 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658133 !Sample_title = healthy cortex cell 263 !Sample_geo_accession = GSM1658133 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486104 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996123 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658133/suppl/GSM1658133_nochipID8.C12.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996123 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658134 !Sample_title = healthy cortex cell 264 !Sample_geo_accession = GSM1658134 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486105 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996124 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658134/suppl/GSM1658134_nochipID8.C13.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996124 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658135 !Sample_title = healthy cortex cell 265 !Sample_geo_accession = GSM1658135 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486106 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996125 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658135/suppl/GSM1658135_nochipID8.C14.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996125 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658136 !Sample_title = healthy cortex cell 266 !Sample_geo_accession = GSM1658136 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486107 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996126 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658136/suppl/GSM1658136_nochipID8.C17.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996126 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658137 !Sample_title = healthy cortex cell 267 !Sample_geo_accession = GSM1658137 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486108 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996127 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658137/suppl/GSM1658137_nochipID8.C19.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996127 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658138 !Sample_title = healthy cortex cell 268 !Sample_geo_accession = GSM1658138 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486109 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996128 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658138/suppl/GSM1658138_nochipID8.C20.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996128 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658139 !Sample_title = healthy cortex cell 269 !Sample_geo_accession = GSM1658139 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486110 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996129 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658139/suppl/GSM1658139_nochipID8.C22.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996129 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658140 !Sample_title = healthy cortex cell 270 !Sample_geo_accession = GSM1658140 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486111 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996130 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658140/suppl/GSM1658140_nochipID8.C23.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996130 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658141 !Sample_title = healthy cortex cell 271 !Sample_geo_accession = GSM1658141 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486112 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996131 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658141/suppl/GSM1658141_nochipID8.C25.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996131 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658142 !Sample_title = healthy cortex cell 272 !Sample_geo_accession = GSM1658142 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486113 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996132 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658142/suppl/GSM1658142_nochipID8.C28.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996132 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658143 !Sample_title = healthy cortex cell 273 !Sample_geo_accession = GSM1658143 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486114 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996133 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658143/suppl/GSM1658143_nochipID8.C29.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996133 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658144 !Sample_title = healthy cortex cell 274 !Sample_geo_accession = GSM1658144 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486115 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996134 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658144/suppl/GSM1658144_nochipID8.C30.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996134 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658145 !Sample_title = healthy cortex cell 275 !Sample_geo_accession = GSM1658145 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486056 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996135 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658145/suppl/GSM1658145_nochipID8.C32.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996135 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658146 !Sample_title = healthy cortex cell 276 !Sample_geo_accession = GSM1658146 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486057 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996136 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658146/suppl/GSM1658146_nochipID8.C36.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996136 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658147 !Sample_title = healthy cortex cell 277 !Sample_geo_accession = GSM1658147 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486058 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996137 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658147/suppl/GSM1658147_nochipID8.C37.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996137 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658148 !Sample_title = healthy cortex cell 278 !Sample_geo_accession = GSM1658148 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486059 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996138 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658148/suppl/GSM1658148_nochipID8.C39.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996138 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658149 !Sample_title = healthy cortex cell 279 !Sample_geo_accession = GSM1658149 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486060 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996139 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658149/suppl/GSM1658149_nochipID8.C40.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996139 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658150 !Sample_title = healthy cortex cell 280 !Sample_geo_accession = GSM1658150 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486061 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996140 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658150/suppl/GSM1658150_nochipID8.C41.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996140 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658151 !Sample_title = healthy cortex cell 281 !Sample_geo_accession = GSM1658151 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486062 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996141 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658151/suppl/GSM1658151_nochipID8.C42.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996141 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658152 !Sample_title = healthy cortex cell 282 !Sample_geo_accession = GSM1658152 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486063 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996142 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658152/suppl/GSM1658152_nochipID8.C43.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996142 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658153 !Sample_title = healthy cortex cell 283 !Sample_geo_accession = GSM1658153 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486064 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996143 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658153/suppl/GSM1658153_nochipID8.C45.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996143 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658154 !Sample_title = healthy cortex cell 284 !Sample_geo_accession = GSM1658154 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486065 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996144 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658154/suppl/GSM1658154_nochipID8.C48.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996144 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658155 !Sample_title = healthy cortex cell 285 !Sample_geo_accession = GSM1658155 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486066 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996145 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658155/suppl/GSM1658155_nochipID8.C49.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996145 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658156 !Sample_title = healthy cortex cell 286 !Sample_geo_accession = GSM1658156 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486067 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996146 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658156/suppl/GSM1658156_nochipID8.C50.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996146 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658157 !Sample_title = healthy cortex cell 287 !Sample_geo_accession = GSM1658157 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486068 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996147 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658157/suppl/GSM1658157_nochipID8.C52.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996147 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658158 !Sample_title = healthy cortex cell 288 !Sample_geo_accession = GSM1658158 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486069 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996148 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658158/suppl/GSM1658158_nochipID8.C53.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996148 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658159 !Sample_title = healthy cortex cell 289 !Sample_geo_accession = GSM1658159 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486070 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996149 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658159/suppl/GSM1658159_nochipID8.C54.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996149 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658160 !Sample_title = healthy cortex cell 290 !Sample_geo_accession = GSM1658160 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486071 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996150 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658160/suppl/GSM1658160_nochipID8.C55.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996150 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658161 !Sample_title = healthy cortex cell 291 !Sample_geo_accession = GSM1658161 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486072 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996151 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658161/suppl/GSM1658161_nochipID8.C56.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996151 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658162 !Sample_title = healthy cortex cell 292 !Sample_geo_accession = GSM1658162 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486073 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996152 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658162/suppl/GSM1658162_nochipID8.C57.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996152 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658163 !Sample_title = healthy cortex cell 293 !Sample_geo_accession = GSM1658163 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486074 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996153 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658163/suppl/GSM1658163_nochipID8.C60.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996153 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658164 !Sample_title = healthy cortex cell 294 !Sample_geo_accession = GSM1658164 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486075 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996154 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658164/suppl/GSM1658164_nochipID8.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996154 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658165 !Sample_title = healthy cortex cell 295 !Sample_geo_accession = GSM1658165 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486076 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996155 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658165/suppl/GSM1658165_nochipID8.C64.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996155 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658166 !Sample_title = healthy cortex cell 296 !Sample_geo_accession = GSM1658166 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486077 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996156 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658166/suppl/GSM1658166_nochipID8.C65.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996156 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658167 !Sample_title = healthy cortex cell 297 !Sample_geo_accession = GSM1658167 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486078 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996157 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658167/suppl/GSM1658167_nochipID8.C66.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996157 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658168 !Sample_title = healthy cortex cell 298 !Sample_geo_accession = GSM1658168 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486085 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996158 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658168/suppl/GSM1658168_nochipID8.C67.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996158 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658169 !Sample_title = healthy cortex cell 299 !Sample_geo_accession = GSM1658169 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486026 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996159 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658169/suppl/GSM1658169_nochipID8.C70.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996159 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658170 !Sample_title = healthy cortex cell 300 !Sample_geo_accession = GSM1658170 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486027 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996160 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658170/suppl/GSM1658170_nochipID8.C75.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996160 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658171 !Sample_title = healthy cortex cell 301 !Sample_geo_accession = GSM1658171 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486079 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996161 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658171/suppl/GSM1658171_nochipID8.C77.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996161 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658172 !Sample_title = healthy cortex cell 302 !Sample_geo_accession = GSM1658172 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486080 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996162 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658172/suppl/GSM1658172_nochipID8.C78.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996162 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658173 !Sample_title = healthy cortex cell 303 !Sample_geo_accession = GSM1658173 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486081 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996163 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658173/suppl/GSM1658173_nochipID8.C79.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996163 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658174 !Sample_title = healthy cortex cell 304 !Sample_geo_accession = GSM1658174 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486082 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996164 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658174/suppl/GSM1658174_nochipID8.C81.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996164 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658175 !Sample_title = healthy cortex cell 305 !Sample_geo_accession = GSM1658175 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486083 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996165 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658175/suppl/GSM1658175_nochipID8.C82.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996165 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658176 !Sample_title = healthy cortex cell 306 !Sample_geo_accession = GSM1658176 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486084 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996166 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658176/suppl/GSM1658176_nochipID8.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996166 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658177 !Sample_title = healthy cortex cell 307 !Sample_geo_accession = GSM1658177 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486028 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996167 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658177/suppl/GSM1658177_nochipID8.C85.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996167 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658178 !Sample_title = healthy cortex cell 308 !Sample_geo_accession = GSM1658178 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486029 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996168 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658178/suppl/GSM1658178_nochipID8.C87.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996168 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658179 !Sample_title = healthy cortex cell 309 !Sample_geo_accession = GSM1658179 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486030 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996169 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658179/suppl/GSM1658179_nochipID8.C88.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996169 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658180 !Sample_title = healthy cortex cell 310 !Sample_geo_accession = GSM1658180 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: oligodendrocytes !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486031 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996170 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658180/suppl/GSM1658180_nochipID8.C90.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996170 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658181 !Sample_title = healthy cortex cell 311 !Sample_geo_accession = GSM1658181 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486032 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996171 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658181/suppl/GSM1658181_nochipID8.C92.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996171 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658182 !Sample_title = healthy cortex cell 312 !Sample_geo_accession = GSM1658182 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486033 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996172 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658182/suppl/GSM1658182_nochipID8.C95.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996172 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658183 !Sample_title = healthy cortex cell 313 !Sample_geo_accession = GSM1658183 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: hybrid !Sample_characteristics_ch1 = age: postnatal 21 years !Sample_characteristics_ch1 = c1 chip id: nochipID8 !Sample_characteristics_ch1 = experiment_sample_name: AB_S7 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486034 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996173 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658183/suppl/GSM1658183_nochipID8.C96.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996173 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658184 !Sample_title = healthy cortex cell 314 !Sample_geo_accession = GSM1658184 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486035 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996174 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658184/suppl/GSM1658184_nochipID9.C01.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996174 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658185 !Sample_title = healthy cortex cell 315 !Sample_geo_accession = GSM1658185 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486036 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996175 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658185/suppl/GSM1658185_nochipID9.C02.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996175 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658186 !Sample_title = healthy cortex cell 316 !Sample_geo_accession = GSM1658186 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486037 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996176 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658186/suppl/GSM1658186_nochipID9.C04.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996176 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658187 !Sample_title = healthy cortex cell 317 !Sample_geo_accession = GSM1658187 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486038 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996177 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658187/suppl/GSM1658187_nochipID9.C09.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996177 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658188 !Sample_title = healthy cortex cell 318 !Sample_geo_accession = GSM1658188 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486039 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996178 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658188/suppl/GSM1658188_nochipID9.C14.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996178 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658189 !Sample_title = healthy cortex cell 319 !Sample_geo_accession = GSM1658189 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486040 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996179 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658189/suppl/GSM1658189_nochipID9.C18.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996179 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658190 !Sample_title = healthy cortex cell 320 !Sample_geo_accession = GSM1658190 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486041 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996180 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658190/suppl/GSM1658190_nochipID9.C26.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996180 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658191 !Sample_title = healthy cortex cell 321 !Sample_geo_accession = GSM1658191 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486042 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996181 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658191/suppl/GSM1658191_nochipID9.C37.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996181 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658192 !Sample_title = healthy cortex cell 322 !Sample_geo_accession = GSM1658192 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486043 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996182 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658192/suppl/GSM1658192_nochipID9.C42.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996182 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658193 !Sample_title = healthy cortex cell 323 !Sample_geo_accession = GSM1658193 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486045 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996183 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658193/suppl/GSM1658193_nochipID9.C57.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996183 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658194 !Sample_title = healthy cortex cell 324 !Sample_geo_accession = GSM1658194 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486046 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996184 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658194/suppl/GSM1658194_nochipID9.C59.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996184 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658195 !Sample_title = healthy cortex cell 325 !Sample_geo_accession = GSM1658195 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486047 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996185 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658195/suppl/GSM1658195_nochipID9.C62.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996185 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658196 !Sample_title = healthy cortex cell 326 !Sample_geo_accession = GSM1658196 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: microglia !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486048 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996186 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658196/suppl/GSM1658196_nochipID9.C65.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996186 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658197 !Sample_title = healthy cortex cell 327 !Sample_geo_accession = GSM1658197 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486049 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996187 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658197/suppl/GSM1658197_nochipID9.C74.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996187 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658198 !Sample_title = healthy cortex cell 328 !Sample_geo_accession = GSM1658198 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486050 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996188 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658198/suppl/GSM1658198_nochipID9.C75.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996188 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658199 !Sample_title = healthy cortex cell 329 !Sample_geo_accession = GSM1658199 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486051 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996189 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658199/suppl/GSM1658199_nochipID9.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996189 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658200 !Sample_title = healthy cortex cell 330 !Sample_geo_accession = GSM1658200 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: neurons !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486052 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996190 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658200/suppl/GSM1658200_nochipID9.C85.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996190 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658201 !Sample_title = healthy cortex cell 331 !Sample_geo_accession = GSM1658201 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486044 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996191 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658201/suppl/GSM1658201_nochipID9.C87.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996191 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658202 !Sample_title = healthy cortex cell 332 !Sample_geo_accession = GSM1658202 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: astrocytes !Sample_characteristics_ch1 = age: postnatal 47 years !Sample_characteristics_ch1 = c1 chip id: nochipID9 !Sample_characteristics_ch1 = experiment_sample_name: AB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486053 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996192 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658202/suppl/GSM1658202_nochipID9.C92.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996192 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658203 !Sample_title = healthy cortex cell 333 !Sample_geo_accession = GSM1658203 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486054 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996193 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658203/suppl/GSM1658203_nochipID10.C02.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996193 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658204 !Sample_title = healthy cortex cell 334 !Sample_geo_accession = GSM1658204 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486055 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996194 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658204/suppl/GSM1658204_nochipID10.C03.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996194 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658205 !Sample_title = healthy cortex cell 335 !Sample_geo_accession = GSM1658205 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485996 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996195 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658205/suppl/GSM1658205_nochipID10.C05.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996195 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658206 !Sample_title = healthy cortex cell 336 !Sample_geo_accession = GSM1658206 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485997 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996196 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658206/suppl/GSM1658206_nochipID10.C07.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996196 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658207 !Sample_title = healthy cortex cell 337 !Sample_geo_accession = GSM1658207 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485998 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996197 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658207/suppl/GSM1658207_nochipID10.C11.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996197 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658208 !Sample_title = healthy cortex cell 338 !Sample_geo_accession = GSM1658208 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485999 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996198 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658208/suppl/GSM1658208_nochipID10.C16.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996198 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658209 !Sample_title = healthy cortex cell 339 !Sample_geo_accession = GSM1658209 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486000 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996199 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658209/suppl/GSM1658209_nochipID10.C17.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996199 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658210 !Sample_title = healthy cortex cell 340 !Sample_geo_accession = GSM1658210 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486001 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996200 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658210/suppl/GSM1658210_nochipID10.C19.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996200 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658211 !Sample_title = healthy cortex cell 341 !Sample_geo_accession = GSM1658211 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486002 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996201 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658211/suppl/GSM1658211_nochipID10.C25.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996201 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658212 !Sample_title = healthy cortex cell 342 !Sample_geo_accession = GSM1658212 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486003 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996202 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658212/suppl/GSM1658212_nochipID10.C26.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996202 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658213 !Sample_title = healthy cortex cell 343 !Sample_geo_accession = GSM1658213 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486004 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996203 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658213/suppl/GSM1658213_nochipID10.C37.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996203 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658214 !Sample_title = healthy cortex cell 344 !Sample_geo_accession = GSM1658214 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486005 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996204 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658214/suppl/GSM1658214_nochipID10.C39.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996204 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658215 !Sample_title = healthy cortex cell 345 !Sample_geo_accession = GSM1658215 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486006 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996205 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658215/suppl/GSM1658215_nochipID10.C42.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996205 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658216 !Sample_title = healthy cortex cell 346 !Sample_geo_accession = GSM1658216 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486007 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996206 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658216/suppl/GSM1658216_nochipID10.C44.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996206 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658217 !Sample_title = healthy cortex cell 347 !Sample_geo_accession = GSM1658217 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486008 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996207 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658217/suppl/GSM1658217_nochipID10.C47.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996207 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658218 !Sample_title = healthy cortex cell 348 !Sample_geo_accession = GSM1658218 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486009 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996208 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658218/suppl/GSM1658218_nochipID10.C49.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996208 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658219 !Sample_title = healthy cortex cell 349 !Sample_geo_accession = GSM1658219 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486010 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996209 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658219/suppl/GSM1658219_nochipID10.C50.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996209 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658220 !Sample_title = healthy cortex cell 350 !Sample_geo_accession = GSM1658220 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486011 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996210 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658220/suppl/GSM1658220_nochipID10.C53.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996210 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658221 !Sample_title = healthy cortex cell 351 !Sample_geo_accession = GSM1658221 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486012 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996211 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658221/suppl/GSM1658221_nochipID10.C58.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996211 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658222 !Sample_title = healthy cortex cell 352 !Sample_geo_accession = GSM1658222 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486013 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996212 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658222/suppl/GSM1658222_nochipID10.C65.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996212 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658223 !Sample_title = healthy cortex cell 353 !Sample_geo_accession = GSM1658223 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486014 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996213 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658223/suppl/GSM1658223_nochipID10.C74.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996213 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658224 !Sample_title = healthy cortex cell 354 !Sample_geo_accession = GSM1658224 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486015 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996214 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658224/suppl/GSM1658224_nochipID10.C75.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996214 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658225 !Sample_title = healthy cortex cell 355 !Sample_geo_accession = GSM1658225 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486016 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996215 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658225/suppl/GSM1658225_nochipID10.C85.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996215 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658226 !Sample_title = healthy cortex cell 356 !Sample_geo_accession = GSM1658226 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486017 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996216 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658226/suppl/GSM1658226_nochipID10.C88.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996216 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658227 !Sample_title = healthy cortex cell 357 !Sample_geo_accession = GSM1658227 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486018 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996217 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658227/suppl/GSM1658227_nochipID10.C93.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996217 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658228 !Sample_title = healthy cortex cell 358 !Sample_geo_accession = GSM1658228 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID10 !Sample_characteristics_ch1 = experiment_sample_name: FB_S1 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486019 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996218 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658228/suppl/GSM1658228_nochipID10.C94.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996218 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658229 !Sample_title = healthy cortex cell 359 !Sample_geo_accession = GSM1658229 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485967 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996219 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658229/suppl/GSM1658229_nochipID11.C02.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996219 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658230 !Sample_title = healthy cortex cell 360 !Sample_geo_accession = GSM1658230 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485968 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996220 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658230/suppl/GSM1658230_nochipID11.C03.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996220 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658231 !Sample_title = healthy cortex cell 361 !Sample_geo_accession = GSM1658231 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486020 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996221 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658231/suppl/GSM1658231_nochipID11.C06.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996221 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658232 !Sample_title = healthy cortex cell 362 !Sample_geo_accession = GSM1658232 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486021 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996222 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658232/suppl/GSM1658232_nochipID11.C07.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996222 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658233 !Sample_title = healthy cortex cell 363 !Sample_geo_accession = GSM1658233 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486022 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996223 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658233/suppl/GSM1658233_nochipID11.C08.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996223 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658234 !Sample_title = healthy cortex cell 364 !Sample_geo_accession = GSM1658234 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486023 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996224 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658234/suppl/GSM1658234_nochipID11.C10.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996224 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658235 !Sample_title = healthy cortex cell 365 !Sample_geo_accession = GSM1658235 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486024 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996225 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658235/suppl/GSM1658235_nochipID11.C15.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996225 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658236 !Sample_title = healthy cortex cell 366 !Sample_geo_accession = GSM1658236 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03486025 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996226 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658236/suppl/GSM1658236_nochipID11.C17.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996226 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658237 !Sample_title = healthy cortex cell 367 !Sample_geo_accession = GSM1658237 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485966 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996227 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658237/suppl/GSM1658237_nochipID11.C19.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996227 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658238 !Sample_title = healthy cortex cell 368 !Sample_geo_accession = GSM1658238 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485969 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996228 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658238/suppl/GSM1658238_nochipID11.C20.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996228 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658239 !Sample_title = healthy cortex cell 369 !Sample_geo_accession = GSM1658239 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485970 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996229 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658239/suppl/GSM1658239_nochipID11.C21.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996229 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658240 !Sample_title = healthy cortex cell 370 !Sample_geo_accession = GSM1658240 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485971 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996230 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658240/suppl/GSM1658240_nochipID11.C22.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996230 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658241 !Sample_title = healthy cortex cell 371 !Sample_geo_accession = GSM1658241 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485972 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996231 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658241/suppl/GSM1658241_nochipID11.C23.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996231 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658242 !Sample_title = healthy cortex cell 372 !Sample_geo_accession = GSM1658242 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485973 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996232 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658242/suppl/GSM1658242_nochipID11.C25.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996232 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658243 !Sample_title = healthy cortex cell 373 !Sample_geo_accession = GSM1658243 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485974 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996233 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658243/suppl/GSM1658243_nochipID11.C30.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996233 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658244 !Sample_title = healthy cortex cell 374 !Sample_geo_accession = GSM1658244 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485975 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996234 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658244/suppl/GSM1658244_nochipID11.C37.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996234 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658245 !Sample_title = healthy cortex cell 375 !Sample_geo_accession = GSM1658245 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485976 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996235 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658245/suppl/GSM1658245_nochipID11.C48.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996235 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658246 !Sample_title = healthy cortex cell 376 !Sample_geo_accession = GSM1658246 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485977 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996236 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658246/suppl/GSM1658246_nochipID11.C49.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996236 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658247 !Sample_title = healthy cortex cell 377 !Sample_geo_accession = GSM1658247 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485978 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996237 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658247/suppl/GSM1658247_nochipID11.C50.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996237 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658248 !Sample_title = healthy cortex cell 378 !Sample_geo_accession = GSM1658248 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485979 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996238 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658248/suppl/GSM1658248_nochipID11.C53.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996238 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658249 !Sample_title = healthy cortex cell 379 !Sample_geo_accession = GSM1658249 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485980 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996239 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658249/suppl/GSM1658249_nochipID11.C54.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996239 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658251 !Sample_title = healthy cortex cell 380 !Sample_geo_accession = GSM1658251 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485981 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996240 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658251/suppl/GSM1658251_nochipID11.C55.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996240 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658253 !Sample_title = healthy cortex cell 381 !Sample_geo_accession = GSM1658253 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485982 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996241 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658253/suppl/GSM1658253_nochipID11.C56.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996241 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658255 !Sample_title = healthy cortex cell 382 !Sample_geo_accession = GSM1658255 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485983 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996242 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658255/suppl/GSM1658255_nochipID11.C57.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996242 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658257 !Sample_title = healthy cortex cell 383 !Sample_geo_accession = GSM1658257 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485984 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996243 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658257/suppl/GSM1658257_nochipID11.C58.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996243 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658259 !Sample_title = healthy cortex cell 384 !Sample_geo_accession = GSM1658259 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485985 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996244 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658259/suppl/GSM1658259_nochipID11.C59.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996244 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658262 !Sample_title = healthy cortex cell 385 !Sample_geo_accession = GSM1658262 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485986 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996245 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658262/suppl/GSM1658262_nochipID11.C60.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996245 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658264 !Sample_title = healthy cortex cell 386 !Sample_geo_accession = GSM1658264 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485987 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996246 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658264/suppl/GSM1658264_nochipID11.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996246 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658266 !Sample_title = healthy cortex cell 387 !Sample_geo_accession = GSM1658266 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485988 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996247 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658266/suppl/GSM1658266_nochipID11.C62.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996247 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658268 !Sample_title = healthy cortex cell 388 !Sample_geo_accession = GSM1658268 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485989 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996248 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658268/suppl/GSM1658268_nochipID11.C63.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996248 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658270 !Sample_title = healthy cortex cell 389 !Sample_geo_accession = GSM1658270 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485990 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996249 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658270/suppl/GSM1658270_nochipID11.C64.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996249 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658272 !Sample_title = healthy cortex cell 390 !Sample_geo_accession = GSM1658272 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485991 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996250 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658272/suppl/GSM1658272_nochipID11.C66.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996250 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658275 !Sample_title = healthy cortex cell 391 !Sample_geo_accession = GSM1658275 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485992 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996251 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658275/suppl/GSM1658275_nochipID11.C68.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996251 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658277 !Sample_title = healthy cortex cell 392 !Sample_geo_accession = GSM1658277 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485993 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996252 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658277/suppl/GSM1658277_nochipID11.C69.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996252 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658279 !Sample_title = healthy cortex cell 393 !Sample_geo_accession = GSM1658279 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485994 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996253 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658279/suppl/GSM1658279_nochipID11.C75.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996253 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658281 !Sample_title = healthy cortex cell 394 !Sample_geo_accession = GSM1658281 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485995 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996254 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658281/suppl/GSM1658281_nochipID11.C76.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996254 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658284 !Sample_title = healthy cortex cell 395 !Sample_geo_accession = GSM1658284 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485936 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996255 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658284/suppl/GSM1658284_nochipID11.C77.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996255 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658286 !Sample_title = healthy cortex cell 396 !Sample_geo_accession = GSM1658286 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485937 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996256 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658286/suppl/GSM1658286_nochipID11.C78.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996256 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658288 !Sample_title = healthy cortex cell 397 !Sample_geo_accession = GSM1658288 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485938 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996257 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658288/suppl/GSM1658288_nochipID11.C79.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996257 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658290 !Sample_title = healthy cortex cell 398 !Sample_geo_accession = GSM1658290 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485939 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996258 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658290/suppl/GSM1658290_nochipID11.C81.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996258 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658292 !Sample_title = healthy cortex cell 399 !Sample_geo_accession = GSM1658292 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485940 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996259 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658292/suppl/GSM1658292_nochipID11.C82.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996259 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658294 !Sample_title = healthy cortex cell 400 !Sample_geo_accession = GSM1658294 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485941 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996260 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658294/suppl/GSM1658294_nochipID11.C83.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996260 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658297 !Sample_title = healthy cortex cell 401 !Sample_geo_accession = GSM1658297 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485942 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996261 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658297/suppl/GSM1658297_nochipID11.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996261 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658299 !Sample_title = healthy cortex cell 402 !Sample_geo_accession = GSM1658299 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485943 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996262 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658299/suppl/GSM1658299_nochipID11.C86.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996262 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658301 !Sample_title = healthy cortex cell 403 !Sample_geo_accession = GSM1658301 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485944 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996263 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658301/suppl/GSM1658301_nochipID11.C91.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996263 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658304 !Sample_title = healthy cortex cell 404 !Sample_geo_accession = GSM1658304 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID11 !Sample_characteristics_ch1 = experiment_sample_name: FB_S2 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485945 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996264 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658304/suppl/GSM1658304_nochipID11.C93.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996264 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658305 !Sample_title = healthy cortex cell 405 !Sample_geo_accession = GSM1658305 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485946 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996265 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658305/suppl/GSM1658305_nochipID13.C07.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996265 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658306 !Sample_title = healthy cortex cell 406 !Sample_geo_accession = GSM1658306 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485947 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996266 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658306/suppl/GSM1658306_nochipID13.C11.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996266 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658307 !Sample_title = healthy cortex cell 407 !Sample_geo_accession = GSM1658307 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485948 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996267 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658307/suppl/GSM1658307_nochipID13.C12.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996267 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658308 !Sample_title = healthy cortex cell 408 !Sample_geo_accession = GSM1658308 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485949 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996268 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658308/suppl/GSM1658308_nochipID13.C14.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996268 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658309 !Sample_title = healthy cortex cell 409 !Sample_geo_accession = GSM1658309 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485950 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996269 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658309/suppl/GSM1658309_nochipID13.C15.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996269 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658310 !Sample_title = healthy cortex cell 410 !Sample_geo_accession = GSM1658310 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485951 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996270 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658310/suppl/GSM1658310_nochipID13.C17.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996270 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658311 !Sample_title = healthy cortex cell 411 !Sample_geo_accession = GSM1658311 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485952 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996271 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658311/suppl/GSM1658311_nochipID13.C21.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996271 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658312 !Sample_title = healthy cortex cell 412 !Sample_geo_accession = GSM1658312 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485953 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996272 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658312/suppl/GSM1658312_nochipID13.C25.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996272 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658313 !Sample_title = healthy cortex cell 413 !Sample_geo_accession = GSM1658313 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485954 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996273 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658313/suppl/GSM1658313_nochipID13.C28.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996273 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658314 !Sample_title = healthy cortex cell 414 !Sample_geo_accession = GSM1658314 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485955 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996274 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658314/suppl/GSM1658314_nochipID13.C32.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996274 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658315 !Sample_title = healthy cortex cell 415 !Sample_geo_accession = GSM1658315 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485956 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996275 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658315/suppl/GSM1658315_nochipID13.C36.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996275 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658316 !Sample_title = healthy cortex cell 416 !Sample_geo_accession = GSM1658316 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485957 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996276 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658316/suppl/GSM1658316_nochipID13.C45.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996276 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658317 !Sample_title = healthy cortex cell 417 !Sample_geo_accession = GSM1658317 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485958 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996277 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658317/suppl/GSM1658317_nochipID13.C46.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996277 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658318 !Sample_title = healthy cortex cell 418 !Sample_geo_accession = GSM1658318 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485959 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996278 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658318/suppl/GSM1658318_nochipID13.C48.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996278 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658319 !Sample_title = healthy cortex cell 419 !Sample_geo_accession = GSM1658319 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485960 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996279 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658319/suppl/GSM1658319_nochipID13.C50.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996279 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658320 !Sample_title = healthy cortex cell 420 !Sample_geo_accession = GSM1658320 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485961 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996280 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658320/suppl/GSM1658320_nochipID13.C55.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996280 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658321 !Sample_title = healthy cortex cell 421 !Sample_geo_accession = GSM1658321 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485962 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996281 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658321/suppl/GSM1658321_nochipID13.C57.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996281 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658322 !Sample_title = healthy cortex cell 422 !Sample_geo_accession = GSM1658322 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485963 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996282 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658322/suppl/GSM1658322_nochipID13.C58.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996282 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658323 !Sample_title = healthy cortex cell 423 !Sample_geo_accession = GSM1658323 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485964 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996283 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658323/suppl/GSM1658323_nochipID13.C59.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996283 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658324 !Sample_title = healthy cortex cell 424 !Sample_geo_accession = GSM1658324 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485965 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996284 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658324/suppl/GSM1658324_nochipID13.C61.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996284 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658325 !Sample_title = healthy cortex cell 425 !Sample_geo_accession = GSM1658325 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485906 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996285 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658325/suppl/GSM1658325_nochipID13.C63.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996285 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658326 !Sample_title = healthy cortex cell 426 !Sample_geo_accession = GSM1658326 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485907 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996286 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658326/suppl/GSM1658326_nochipID13.C64.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996286 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658327 !Sample_title = healthy cortex cell 427 !Sample_geo_accession = GSM1658327 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485908 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996287 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658327/suppl/GSM1658327_nochipID13.C66.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996287 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658328 !Sample_title = healthy cortex cell 428 !Sample_geo_accession = GSM1658328 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485909 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996288 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658328/suppl/GSM1658328_nochipID13.C67.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996288 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658329 !Sample_title = healthy cortex cell 429 !Sample_geo_accession = GSM1658329 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485910 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996289 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658329/suppl/GSM1658329_nochipID13.C68.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996289 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658330 !Sample_title = healthy cortex cell 430 !Sample_geo_accession = GSM1658330 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485911 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996290 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658330/suppl/GSM1658330_nochipID13.C72.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996290 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658331 !Sample_title = healthy cortex cell 431 !Sample_geo_accession = GSM1658331 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485912 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996291 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658331/suppl/GSM1658331_nochipID13.C73.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996291 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658332 !Sample_title = healthy cortex cell 432 !Sample_geo_accession = GSM1658332 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485913 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996292 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658332/suppl/GSM1658332_nochipID13.C74.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996292 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658333 !Sample_title = healthy cortex cell 433 !Sample_geo_accession = GSM1658333 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485914 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996293 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658333/suppl/GSM1658333_nochipID13.C75.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996293 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658334 !Sample_title = healthy cortex cell 434 !Sample_geo_accession = GSM1658334 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485915 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996294 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658334/suppl/GSM1658334_nochipID13.C80.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996294 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658335 !Sample_title = healthy cortex cell 435 !Sample_geo_accession = GSM1658335 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485916 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996295 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658335/suppl/GSM1658335_nochipID13.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996295 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658336 !Sample_title = healthy cortex cell 436 !Sample_geo_accession = GSM1658336 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485917 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996296 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658336/suppl/GSM1658336_nochipID13.C87.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996296 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658337 !Sample_title = healthy cortex cell 437 !Sample_geo_accession = GSM1658337 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID13 !Sample_characteristics_ch1 = experiment_sample_name: FB_S3 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL15520 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina MiSeq !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485918 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996297 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658337/suppl/GSM1658337_nochipID13.C93.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996297 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658338 !Sample_title = healthy cortex cell 438 !Sample_geo_accession = GSM1658338 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485919 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996298 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658338/suppl/GSM1658338_nochipID4.C03.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996298 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658339 !Sample_title = healthy cortex cell 439 !Sample_geo_accession = GSM1658339 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485920 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996299 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658339/suppl/GSM1658339_nochipID4.C04.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996299 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658340 !Sample_title = healthy cortex cell 440 !Sample_geo_accession = GSM1658340 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485921 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996300 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658340/suppl/GSM1658340_nochipID4.C10.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996300 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658341 !Sample_title = healthy cortex cell 441 !Sample_geo_accession = GSM1658341 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485922 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996301 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658341/suppl/GSM1658341_nochipID4.C14.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996301 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658342 !Sample_title = healthy cortex cell 442 !Sample_geo_accession = GSM1658342 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485923 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996302 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658342/suppl/GSM1658342_nochipID4.C18.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996302 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658343 !Sample_title = healthy cortex cell 443 !Sample_geo_accession = GSM1658343 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485924 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996303 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658343/suppl/GSM1658343_nochipID4.C19.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996303 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658344 !Sample_title = healthy cortex cell 444 !Sample_geo_accession = GSM1658344 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485925 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996304 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658344/suppl/GSM1658344_nochipID4.C20.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996304 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658345 !Sample_title = healthy cortex cell 445 !Sample_geo_accession = GSM1658345 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485929 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996305 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658345/suppl/GSM1658345_nochipID4.C21.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996305 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658346 !Sample_title = healthy cortex cell 446 !Sample_geo_accession = GSM1658346 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485930 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996306 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658346/suppl/GSM1658346_nochipID4.C33.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996306 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658347 !Sample_title = healthy cortex cell 447 !Sample_geo_accession = GSM1658347 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485931 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996307 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658347/suppl/GSM1658347_nochipID4.C34.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996307 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658348 !Sample_title = healthy cortex cell 448 !Sample_geo_accession = GSM1658348 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485932 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996308 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658348/suppl/GSM1658348_nochipID4.C38.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996308 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658349 !Sample_title = healthy cortex cell 449 !Sample_geo_accession = GSM1658349 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485933 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996309 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658349/suppl/GSM1658349_nochipID4.C39.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996309 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658350 !Sample_title = healthy cortex cell 450 !Sample_geo_accession = GSM1658350 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485934 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996310 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658350/suppl/GSM1658350_nochipID4.C41.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996310 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658351 !Sample_title = healthy cortex cell 451 !Sample_geo_accession = GSM1658351 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485926 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996311 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658351/suppl/GSM1658351_nochipID4.C42.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996311 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658352 !Sample_title = healthy cortex cell 452 !Sample_geo_accession = GSM1658352 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485927 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996312 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658352/suppl/GSM1658352_nochipID4.C44.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996312 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658353 !Sample_title = healthy cortex cell 453 !Sample_geo_accession = GSM1658353 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485928 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996313 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658353/suppl/GSM1658353_nochipID4.C49.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996313 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658354 !Sample_title = healthy cortex cell 454 !Sample_geo_accession = GSM1658354 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485935 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996314 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658354/suppl/GSM1658354_nochipID4.C52.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996314 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658355 !Sample_title = healthy cortex cell 455 !Sample_geo_accession = GSM1658355 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_replicating !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485894 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996315 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658355/suppl/GSM1658355_nochipID4.C53.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996315 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658356 !Sample_title = healthy cortex cell 456 !Sample_geo_accession = GSM1658356 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485895 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996316 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658356/suppl/GSM1658356_nochipID4.C59.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996316 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658357 !Sample_title = healthy cortex cell 457 !Sample_geo_accession = GSM1658357 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485896 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996317 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658357/suppl/GSM1658357_nochipID4.C62.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996317 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658358 !Sample_title = healthy cortex cell 458 !Sample_geo_accession = GSM1658358 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485897 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996318 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658358/suppl/GSM1658358_nochipID4.C63.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996318 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658359 !Sample_title = healthy cortex cell 459 !Sample_geo_accession = GSM1658359 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485898 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996319 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658359/suppl/GSM1658359_nochipID4.C66.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996319 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658360 !Sample_title = healthy cortex cell 460 !Sample_geo_accession = GSM1658360 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485899 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996320 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658360/suppl/GSM1658360_nochipID4.C74.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996320 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658361 !Sample_title = healthy cortex cell 461 !Sample_geo_accession = GSM1658361 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485900 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996321 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658361/suppl/GSM1658361_nochipID4.C77.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996321 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658362 !Sample_title = healthy cortex cell 462 !Sample_geo_accession = GSM1658362 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485901 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996322 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658362/suppl/GSM1658362_nochipID4.C78.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996322 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658363 !Sample_title = healthy cortex cell 463 !Sample_geo_accession = GSM1658363 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485902 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996323 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658363/suppl/GSM1658363_nochipID4.C84.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996323 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658364 !Sample_title = healthy cortex cell 464 !Sample_geo_accession = GSM1658364 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485903 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996324 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658364/suppl/GSM1658364_nochipID4.C89.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996324 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658365 !Sample_title = healthy cortex cell 465 !Sample_geo_accession = GSM1658365 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485904 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996325 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658365/suppl/GSM1658365_nochipID4.C95.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996325 !Sample_series_id = GSE67835 !Sample_data_row_count = 0 ^SAMPLE = GSM1658366 !Sample_title = healthy cortex cell 466 !Sample_geo_accession = GSM1658366 !Sample_status = Public on May 20 2015 !Sample_submission_date = Apr 15 2015 !Sample_last_update_date = Nov 06 2015 !Sample_type = SRA !Sample_channel_count = 1 !Sample_source_name_ch1 = Brain !Sample_organism_ch1 = Homo sapiens !Sample_taxid_ch1 = 9606 !Sample_characteristics_ch1 = tissue: cortex !Sample_characteristics_ch1 = cell type: fetal_quiescent !Sample_characteristics_ch1 = age: prenatal 16-18 W !Sample_characteristics_ch1 = c1 chip id: nochipID4 !Sample_characteristics_ch1 = experiment_sample_name: FB_S6 !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = C1 autoprep standard protocol !Sample_extract_protocol_ch1 = C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol !Sample_extract_protocol_ch1 = Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system. !Sample_description = Single cell from healthy human cortex !Sample_data_processing = Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). !Sample_data_processing = Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). !Sample_data_processing = Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). !Sample_data_processing = Genome_build: hg19 !Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample !Sample_platform_id = GPL18573 !Sample_contact_name = Martin,,Enge !Sample_contact_email = martin.enge@ki.se !Sample_contact_department = Dep of Oncology-Pathology !Sample_contact_institute = Karolinska Institute !Sample_contact_address = CCK, Z4 !Sample_contact_city = Stockholm !Sample_contact_zip/postal_code = S-171 76 !Sample_contact_country = Sweden !Sample_instrument_model = Illumina NextSeq 500 !Sample_library_selection = cDNA !Sample_library_source = transcriptomic !Sample_library_strategy = RNA-Seq !Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03485905 !Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX996326 !Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658366/suppl/GSM1658366_nochipID4.C96.csv.gz !Sample_supplementary_file_2 = ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996326 !Sample_series_id = GSE67835 !Sample_data_row_count = 0