"title" "geo_accession" "status" "submission_date" "last_update_date" "type" "channel_count" "source_name_ch1" "organism_ch1" "characteristics_ch1" "characteristics_ch1.1" "characteristics_ch1.2" "characteristics_ch1.3" "characteristics_ch1.4" "molecule_ch1" "extract_protocol_ch1" "extract_protocol_ch1.1" "extract_protocol_ch1.2" "taxid_ch1" "description" "data_processing" "data_processing.1" "data_processing.2" "data_processing.3" "data_processing.4" "platform_id" "contact_name" "contact_email" "contact_laboratory" "contact_department" "contact_institute" "contact_address" "contact_city" "contact_zip/postal_code" "contact_country" "data_row_count" "instrument_model" "library_selection" "library_source" "library_strategy" "relation" "relation.1" "supplementary_file_1" "supplementary_file_2" "file" "SeqInstrument" "ChipID" "BrainRegion" "CellClass" "Age" "AgeJTRf" "AgeJTRfJTR" "SampleName" "colorBYage" "colorBYregion" "colorBYcellClass" "pchBYcellClass" "pchBYage" "colorBYinstrumnt" "colorBYchipID" "colorBYsample" "no.feature" "ambiguous" "alignment.not.unique" "X" "colorBYdcx" "healthy cortex cell 1" "GSM1657871" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486326" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995861" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657871/GSM1657871_1772078217.C03.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995861" "GSM1657871_1772078217.C03.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 54.6798946727067 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 822062 5663 697959 54.6798946727067 "#0000FFFF" "healthy cortex cell 2" "GSM1657872" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486327" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995862" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657872/GSM1657872_1772078217.C04.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995862" "GSM1657872_1772078217.C04.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 54.9376901984215 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 970221 5771 847047 54.9376901984215 "#0000FFFF" "healthy cortex cell 3" "GSM1657873" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486328" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995863" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657873/GSM1657873_1772078217.C06.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995863" "GSM1657873_1772078217.C06.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 55.0918717375025 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 952904 7831 613329 55.0918717375025 "#0000FFFF" "healthy cortex cell 4" "GSM1657874" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486329" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995864" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657874/GSM1657874_1772078217.C07.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995864" "GSM1657874_1772078217.C07.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 56.1228131363168 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 1301729 4780 742635 56.1228131363168 "#0000FFFF" "healthy cortex cell 5" "GSM1657875" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486330" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995865" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657875/GSM1657875_1772078217.C08.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995865" "GSM1657875_1772078217.C08.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 54.197162120603 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 882830 5002 765874 54.197162120603 "#0000FFFF" "healthy cortex cell 6" "GSM1657876" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486331" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995866" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657876/GSM1657876_1772078217.C09.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995866" "GSM1657876_1772078217.C09.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 56.4509277902544 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 1098392 2388 1118933 56.4509277902544 "#4100BEFF" "healthy cortex cell 7" "GSM1657877" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486332" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995867" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657877/GSM1657877_1772078217.C14.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995867" "GSM1657877_1772078217.C14.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 54.9247911069542 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 768831 10386 556215 54.9247911069542 "#0000FFFF" "healthy cortex cell 8" "GSM1657878" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486333" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995868" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657878/GSM1657878_1772078217.C16.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995868" "GSM1657878_1772078217.C16.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 55.0121026262641 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 1436879 8422 1051949 55.0121026262641 "#5000AFFF" "healthy cortex cell 9" "GSM1657879" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486334" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995869" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657879/GSM1657879_1772078217.C17.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995869" "GSM1657879_1772078217.C17.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 53.0463557587937 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 936055 4667 669653 53.0463557587937 "#4800B7FF" "healthy cortex cell 10" "GSM1657880" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486335" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995870" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657880/GSM1657880_1772078217.C18.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995870" "GSM1657880_1772078217.C18.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 56.4594617849216 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 729299 11112 584841 56.4594617849216 "#2D00D2FF" "healthy cortex cell 11" "GSM1657881" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486336" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995871" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657881/GSM1657881_1772078217.C20.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995871" "GSM1657881_1772078217.C20.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 56.7436169078574 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 728587 6593 479471 56.7436169078574 "#0000FFFF" "healthy cortex cell 12" "GSM1657882" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486337" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995872" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657882/GSM1657882_1772078217.C23.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995872" "GSM1657882_1772078217.C23.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 53.465463893488 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 1596112 4742 832852 53.465463893488 "#8F0070FF" "healthy cortex cell 13" "GSM1657883" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486338" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995873" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657883/GSM1657883_1772078217.C28.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995873" "GSM1657883_1772078217.C28.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 55.3963571358472 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 1724433 7381 1093286 55.3963571358472 "#74008BFF" "healthy cortex cell 14" "GSM1657884" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486339" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995874" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657884/GSM1657884_1772078217.C29.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995874" "GSM1657884_1772078217.C29.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 54.0387705983594 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 824714 3241 596751 54.0387705983594 "#3E00C1FF" "healthy cortex cell 15" "GSM1657885" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486340" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995875" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657885/GSM1657885_1772078217.C32.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995875" "GSM1657885_1772078217.C32.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "astrocytes" 54 54 56.0734632257372 "AB_S8" 8 2 "yellow" 22 9 2 "#8A2BE2FF" "#FFA500FF" 1182447 7469 863002 56.0734632257372 "#0000FFFF" "healthy cortex cell 16" "GSM1657886" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486341" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995876" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657886/GSM1657886_1772078217.C33.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995876" "GSM1657886_1772078217.C33.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 53.6797028668225 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 2116891 8834 1344800 53.6797028668225 "#72008DFF" "healthy cortex cell 17" "GSM1657887" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486342" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995877" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657887/GSM1657887_1772078217.C39.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995877" "GSM1657887_1772078217.C39.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 56.1505484078079 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 2091618 9460 1369670 56.1505484078079 "#A0005FFF" "healthy cortex cell 18" "GSM1657888" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486343" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995878" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657888/GSM1657888_1772078217.C40.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995878" "GSM1657888_1772078217.C40.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 54.0956103689969 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 1512735 7355 751340 54.0956103689969 "#4E00B1FF" "healthy cortex cell 19" "GSM1657889" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486344" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995879" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657889/GSM1657889_1772078217.C47.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995879" "GSM1657889_1772078217.C47.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 54.3424201551825 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 898243 11551 752573 54.3424201551825 "#0000FFFF" "healthy cortex cell 20" "GSM1657890" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486358" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995880" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657890/GSM1657890_1772078217.C52.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995880" "GSM1657890_1772078217.C52.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 54.858523757197 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 1074461 5534 443409 54.858523757197 "#1400EBFF" "healthy cortex cell 21" "GSM1657891" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486355" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995881" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657891/GSM1657891_1772078217.C56.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995881" "GSM1657891_1772078217.C56.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 55.5187194850296 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 734120 9076 549085 55.5187194850296 "#0000FFFF" "healthy cortex cell 22" "GSM1657892" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486356" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995882" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657892/GSM1657892_1772078217.C58.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995882" "GSM1657892_1772078217.C58.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 54.7473750477657 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 832691 5166 605574 54.7473750477657 "#0000FFFF" "healthy cortex cell 23" "GSM1657893" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486357" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995883" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657893/GSM1657893_1772078217.C59.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995883" "GSM1657893_1772078217.C59.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "OPC" 54 54 54.9151931954548 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#8A2BE2FF" "#FFA500FF" 1264183 4689 681958 54.9151931954548 "#0000FFFF" "healthy cortex cell 24" "GSM1657894" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486345" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995884" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657894/GSM1657894_1772078217.C60.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995884" "GSM1657894_1772078217.C60.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 53.8097670767456 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 705534 4359 371174 53.8097670767456 "#0000FFFF" "healthy cortex cell 25" "GSM1657895" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486346" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995885" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657895/GSM1657895_1772078217.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995885" "GSM1657895_1772078217.C61.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 53.8089767573401 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 1062478 10784 920363 53.8089767573401 "#CA0035FF" "healthy cortex cell 26" "GSM1657896" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486347" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995886" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657896/GSM1657896_1772078217.C66.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995886" "GSM1657896_1772078217.C66.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 55.4096694951877 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 1649862 3125 1024874 55.4096694951877 "#A4005BFF" "healthy cortex cell 27" "GSM1657897" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486348" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995887" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657897/GSM1657897_1772078217.C72.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995887" "GSM1657897_1772078217.C72.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "hybrid" 54 54 54.8194975107908 "AB_S8" 8 2 "deeppink" 9 9 2 "#8A2BE2FF" "#FFA500FF" 1399839 6407 639336 54.8194975107908 "#0000FFFF" "healthy cortex cell 28" "GSM1657898" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486349" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995888" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657898/GSM1657898_1772078217.C80.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995888" "GSM1657898_1772078217.C80.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 55.6340666608885 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 490423 5652 1093560 55.6340666608885 "#0000FFFF" "healthy cortex cell 29" "GSM1657899" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486350" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995889" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657899/GSM1657899_1772078217.C87.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995889" "GSM1657899_1772078217.C87.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 54.9374661864713 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 1227875 9552 832352 54.9374661864713 "#0000FFFF" "healthy cortex cell 30" "GSM1657900" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486351" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995890" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657900/GSM1657900_1772078217.C89.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995890" "GSM1657900_1772078217.C89.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 54.0231611933559 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 1134365 6462 672107 54.0231611933559 "#0000FFFF" "healthy cortex cell 31" "GSM1657901" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486352" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995891" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657901/GSM1657901_1772078217.C91.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995891" "GSM1657901_1772078217.C91.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 56.3966033961624 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 1228973 7651 759694 56.3966033961624 "#0000FFFF" "healthy cortex cell 32" "GSM1657902" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486353" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995892" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657902/GSM1657902_1772078217.C94.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995892" "GSM1657902_1772078217.C94.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "oligodendrocytes" 54 54 53.9956309013069 "AB_S8" 8 2 "dodgerblue" 24 9 2 "#8A2BE2FF" "#FFA500FF" 786973 9805 462970 53.9956309013069 "#0000FFFF" "healthy cortex cell 33" "GSM1657903" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078217" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486296" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995893" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657903/GSM1657903_1772078217.C96.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995893" "GSM1657903_1772078217.C96.csv" "Illumina NextSeq 500" "1772078217" "TemporalLobe" "OPC" 54 54 53.1386814722791 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#8A2BE2FF" "#FFA500FF" 891367 9772 956696 53.1386814722791 "#0000FFFF" "healthy cortex cell 34" "GSM1657904" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486297" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995894" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657904/GSM1657904_1772078218.C05.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995894" "GSM1657904_1772078218.C05.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 54.9787472952157 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1315229 4153 766212 54.9787472952157 "#0000FFFF" "healthy cortex cell 35" "GSM1657905" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486298" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995895" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657905/GSM1657905_1772078218.C08.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995895" "GSM1657905_1772078218.C08.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "hybrid" 54 54 53.1144815646112 "AB_S8" 8 2 "deeppink" 9 9 2 "#00008BFF" "#FFA500FF" 657241 3112 593462 53.1144815646112 "#0000FFFF" "healthy cortex cell 36" "GSM1657906" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486299" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995896" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657906/GSM1657906_1772078218.C09.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995896" "GSM1657906_1772078218.C09.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 54.2631419599056 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1757795 6813 900927 54.2631419599056 "#0000FFFF" "healthy cortex cell 37" "GSM1657907" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486300" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995897" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657907/GSM1657907_1772078218.C13.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995897" "GSM1657907_1772078218.C13.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 55.1527395453304 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1414241 3329 975251 55.1527395453304 "#0000FFFF" "healthy cortex cell 38" "GSM1657908" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486301" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995898" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657908/GSM1657908_1772078218.C18.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995898" "GSM1657908_1772078218.C18.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 53.7334142336622 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1309298 6162 965357 53.7334142336622 "#0000FFFF" "healthy cortex cell 39" "GSM1657909" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486302" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995899" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657909/GSM1657909_1772078218.C23.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995899" "GSM1657909_1772078218.C23.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 54.3738892497495 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1013430 4109 732284 54.3738892497495 "#0000FFFF" "healthy cortex cell 40" "GSM1657910" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486303" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995900" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657910/GSM1657910_1772078218.C27.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995900" "GSM1657910_1772078218.C27.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "microglia" 54 54 56.0118164895102 "AB_S8" 8 2 "springgreen" 7 9 2 "#00008BFF" "#FFA500FF" 1235727 2953 596815 56.0118164895102 "#0000FFFF" "healthy cortex cell 41" "GSM1657911" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486304" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995901" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657911/GSM1657911_1772078218.C29.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995901" "GSM1657911_1772078218.C29.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 54.7115591010079 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1100609 4257 844888 54.7115591010079 "#0000FFFF" "healthy cortex cell 42" "GSM1657912" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486305" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995902" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657912/GSM1657912_1772078218.C32.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995902" "GSM1657912_1772078218.C32.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "hybrid" 54 54 54.1780295660719 "AB_S8" 8 2 "deeppink" 9 9 2 "#00008BFF" "#FFA500FF" 1050857 6442 895713 54.1780295660719 "#670098FF" "healthy cortex cell 43" "GSM1657913" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486306" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995903" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657913/GSM1657913_1772078218.C34.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995903" "GSM1657913_1772078218.C34.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 53.0114151518792 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1245497 5534 704604 53.0114151518792 "#0000FFFF" "healthy cortex cell 44" "GSM1657914" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486307" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995904" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657914/GSM1657914_1772078218.C43.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995904" "GSM1657914_1772078218.C43.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 55.711138010025 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1088846 5028 1012667 55.711138010025 "#0000FFFF" "healthy cortex cell 45" "GSM1657915" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486308" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995905" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657915/GSM1657915_1772078218.C44.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995905" "GSM1657915_1772078218.C44.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 53.728289659135 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1380616 3991 747428 53.728289659135 "#6A0095FF" "healthy cortex cell 46" "GSM1657916" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486309" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995906" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657916/GSM1657916_1772078218.C47.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995906" "GSM1657916_1772078218.C47.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 55.8758829347789 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1664165 4673 1060344 55.8758829347789 "#0000FFFF" "healthy cortex cell 47" "GSM1657917" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486310" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995907" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657917/GSM1657917_1772078218.C48.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995907" "GSM1657917_1772078218.C48.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 55.1623814627528 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1363866 4731 1023757 55.1623814627528 "#BF0040FF" "healthy cortex cell 48" "GSM1657918" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486311" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995908" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657918/GSM1657918_1772078218.C53.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995908" "GSM1657918_1772078218.C53.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "microglia" 54 54 56.842691632919 "AB_S8" 8 2 "springgreen" 7 9 2 "#00008BFF" "#FFA500FF" 1137369 2839 678799 56.842691632919 "#3700C8FF" "healthy cortex cell 49" "GSM1657919" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486312" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995909" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657919/GSM1657919_1772078218.C55.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995909" "GSM1657919_1772078218.C55.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "microglia" 54 54 55.07344186306 "AB_S8" 8 2 "springgreen" 7 9 2 "#00008BFF" "#FFA500FF" 842684 2403 688465 55.07344186306 "#0000FFFF" "healthy cortex cell 50" "GSM1657920" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486313" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995910" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657920/GSM1657920_1772078218.C56.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995910" "GSM1657920_1772078218.C56.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 55.3401930974796 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1244465 3821 877489 55.3401930974796 "#0000FFFF" "healthy cortex cell 51" "GSM1657921" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486314" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995911" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657921/GSM1657921_1772078218.C58.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995911" "GSM1657921_1772078218.C58.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 56.1497199609876 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1625670 4543 1376819 56.1497199609876 "#0000FFFF" "healthy cortex cell 52" "GSM1657922" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486315" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995912" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657922/GSM1657922_1772078218.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995912" "GSM1657922_1772078218.C61.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 54.859625896439 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1508151 4194 969814 54.859625896439 "#0000FFFF" "healthy cortex cell 53" "GSM1657923" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486316" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995913" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657923/GSM1657923_1772078218.C71.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995913" "GSM1657923_1772078218.C71.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "microglia" 54 54 53.472035526298 "AB_S8" 8 2 "springgreen" 7 9 2 "#00008BFF" "#FFA500FF" 1042552 7888 521951 53.472035526298 "#0000FFFF" "healthy cortex cell 54" "GSM1657924" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486317" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995914" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657924/GSM1657924_1772078218.C85.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995914" "GSM1657924_1772078218.C85.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 54.1520136054605 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1450881 5839 847075 54.1520136054605 "#0000FFFF" "healthy cortex cell 55" "GSM1657925" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486318" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995915" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657925/GSM1657925_1772078218.C88.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995915" "GSM1657925_1772078218.C88.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "microglia" 54 54 56.460129538551 "AB_S8" 8 2 "springgreen" 7 9 2 "#00008BFF" "#FFA500FF" 1322814 3201 775797 56.460129538551 "#0000FFFF" "healthy cortex cell 56" "GSM1657926" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486319" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995916" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657926/GSM1657926_1772078218.C89.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995916" "GSM1657926_1772078218.C89.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "microglia" 54 54 56.1889557735994 "AB_S8" 8 2 "springgreen" 7 9 2 "#00008BFF" "#FFA500FF" 737379 8601 644181 56.1889557735994 "#0000FFFF" "healthy cortex cell 57" "GSM1657927" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486320" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995917" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657927/GSM1657927_1772078218.C93.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995917" "GSM1657927_1772078218.C93.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "microglia" 54 54 54.1580768376589 "AB_S8" 8 2 "springgreen" 7 9 2 "#00008BFF" "#FFA500FF" 564361 5011 597119 54.1580768376589 "#0000FFFF" "healthy cortex cell 58" "GSM1657928" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: OPC" "age: postnatal 54 years" "c1 chip id: 1772078218" "experiment_sample_name: AB_S8" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486321" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995918" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657928/GSM1657928_1772078218.C95.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995918" "GSM1657928_1772078218.C95.csv" "Illumina NextSeq 500" "1772078218" "TemporalLobe" "OPC" 54 54 54.4006680212915 "AB_S8" 8 2 "dodgerblue4" 25 9 2 "#00008BFF" "#FFA500FF" 1228965 4953 832459 54.4006680212915 "#A3005CFF" "healthy cortex cell 59" "GSM1657929" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486322" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995919" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657929/GSM1657929_1772078236.C11.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995919" "GSM1657929_1772078236.C11.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "hybrid" 37 37 36.4051275271922 "AB_S11" 4 2 "deeppink" 9 22 2 "#00008BFF" "#0000FFFF" 1191504 3602 1028271 36.4051275271922 "#0000FFFF" "healthy cortex cell 60" "GSM1657930" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486323" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995920" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657930/GSM1657930_1772078236.C12.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995920" "GSM1657930_1772078236.C12.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 36.3546101292595 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1243694 10962 1014478 36.3546101292595 "#81007EFF" "healthy cortex cell 61" "GSM1657931" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486324" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995921" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657931/GSM1657931_1772078236.C16.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995921" "GSM1657931_1772078236.C16.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 38.3572527123615 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 894317 7026 1053353 38.3572527123615 "#B3004CFF" "healthy cortex cell 62" "GSM1657932" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486325" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995922" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657932/GSM1657932_1772078236.C17.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995922" "GSM1657932_1772078236.C17.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "astrocytes" 37 37 38.0153082553297 "AB_S11" 4 2 "yellow" 22 22 2 "#00008BFF" "#0000FFFF" 911868 8824 766088 38.0153082553297 "#0000FFFF" "healthy cortex cell 63" "GSM1657933" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486359" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995923" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657933/GSM1657933_1772078236.C19.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995923" "GSM1657933_1772078236.C19.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 37.7570736603811 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1895796 8741 1301797 37.7570736603811 "#0000FFFF" "healthy cortex cell 64" "GSM1657934" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486354" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995924" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657934/GSM1657934_1772078236.C25.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995924" "GSM1657934_1772078236.C25.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "microglia" 37 37 38.0687136957422 "AB_S11" 4 2 "springgreen" 7 22 2 "#00008BFF" "#0000FFFF" 1242627 4997 1277426 38.0687136957422 "#0000FFFF" "healthy cortex cell 65" "GSM1657935" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486266" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995925" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657935/GSM1657935_1772078236.C26.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995925" "GSM1657935_1772078236.C26.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.0696559660137 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1811659 8322 1390976 35.0696559660137 "#880077FF" "healthy cortex cell 66" "GSM1657936" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486267" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995926" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657936/GSM1657936_1772078236.C27.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995926" "GSM1657936_1772078236.C27.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "hybrid" 37 37 36.848214622587 "AB_S11" 4 2 "deeppink" 9 22 2 "#00008BFF" "#0000FFFF" 1849560 6159 1148935 36.848214622587 "#3700C8FF" "healthy cortex cell 67" "GSM1657937" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486268" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995927" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657937/GSM1657937_1772078236.C28.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995927" "GSM1657937_1772078236.C28.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 37.0140010714531 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1978862 6153 1273065 37.0140010714531 "#A2005DFF" "healthy cortex cell 68" "GSM1657938" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486269" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995928" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657938/GSM1657938_1772078236.C30.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995928" "GSM1657938_1772078236.C30.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "astrocytes" 37 37 35.4273739093915 "AB_S11" 4 2 "yellow" 22 22 2 "#00008BFF" "#0000FFFF" 1467167 4402 951951 35.4273739093915 "#0000FFFF" "healthy cortex cell 69" "GSM1657939" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486270" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995929" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657939/GSM1657939_1772078236.C31.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995929" "GSM1657939_1772078236.C31.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 38.440339599736 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1127769 4708 1044041 38.440339599736 "#93006CFF" "healthy cortex cell 70" "GSM1657940" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486271" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995930" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657940/GSM1657940_1772078236.C32.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995930" "GSM1657940_1772078236.C32.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 38.9196868464351 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 830353 5252 720799 38.9196868464351 "#0000FFFF" "healthy cortex cell 71" "GSM1657941" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486272" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995931" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657941/GSM1657941_1772078236.C33.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995931" "GSM1657941_1772078236.C33.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.2621633997187 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1193132 2289 751672 35.2621633997187 "#3700C8FF" "healthy cortex cell 72" "GSM1657942" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486273" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995932" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657942/GSM1657942_1772078236.C34.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995932" "GSM1657942_1772078236.C34.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 38.7012198455632 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 839510 6321 809571 38.7012198455632 "#0000FFFF" "healthy cortex cell 73" "GSM1657943" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486274" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995933" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657943/GSM1657943_1772078236.C36.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995933" "GSM1657943_1772078236.C36.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.4993803435937 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1520374 4567 890997 35.4993803435937 "#AA0055FF" "healthy cortex cell 74" "GSM1657944" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486275" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995934" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657944/GSM1657944_1772078236.C38.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995934" "GSM1657944_1772078236.C38.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "oligodendrocytes" 37 37 36.6762061230838 "AB_S11" 4 2 "dodgerblue" 24 22 2 "#00008BFF" "#0000FFFF" 162281 1488 216186 36.6762061230838 "#2700D8FF" "healthy cortex cell 75" "GSM1657945" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486276" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995935" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657945/GSM1657945_1772078236.C40.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995935" "GSM1657945_1772078236.C40.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 36.5757044134662 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1003837 4849 635442 36.5757044134662 "#1400EBFF" "healthy cortex cell 76" "GSM1657946" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486277" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995936" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657946/GSM1657946_1772078236.C41.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995936" "GSM1657946_1772078236.C41.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 38.296495241113 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1303775 10324 1093371 38.296495241113 "#AD0052FF" "healthy cortex cell 77" "GSM1657947" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486278" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995937" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657947/GSM1657947_1772078236.C45.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995937" "GSM1657947_1772078236.C45.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "hybrid" 37 37 35.4656904740259 "AB_S11" 4 2 "deeppink" 9 22 2 "#00008BFF" "#0000FFFF" 1270433 6882 1107477 35.4656904740259 "#3300CCFF" "healthy cortex cell 78" "GSM1657948" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486279" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995938" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657948/GSM1657948_1772078236.C46.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995938" "GSM1657948_1772078236.C46.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 37.2649294128641 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1563311 4655 1134654 37.2649294128641 "#1400EBFF" "healthy cortex cell 79" "GSM1657949" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486280" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995939" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657949/GSM1657949_1772078236.C47.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995939" "GSM1657949_1772078236.C47.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 38.5912725199014 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 463857 3562 374063 38.5912725199014 "#0000FFFF" "healthy cortex cell 80" "GSM1657950" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486281" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995940" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657950/GSM1657950_1772078236.C49.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995940" "GSM1657950_1772078236.C49.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.3436055146158 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1488604 3283 910497 35.3436055146158 "#B4004BFF" "healthy cortex cell 81" "GSM1657951" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486282" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995941" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657951/GSM1657951_1772078236.C54.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995941" "GSM1657951_1772078236.C54.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.8483536560088 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1629597 6069 1095394 35.8483536560088 "#0000FFFF" "healthy cortex cell 82" "GSM1657952" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486283" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995942" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657952/GSM1657952_1772078236.C56.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995942" "GSM1657952_1772078236.C56.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 37.3462740750983 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 2011604 9875 1248441 37.3462740750983 "#0000FFFF" "healthy cortex cell 83" "GSM1657953" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486284" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995943" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657953/GSM1657953_1772078236.C57.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995943" "GSM1657953_1772078236.C57.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.0355001846328 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 129646 4219 182674 35.0355001846328 "#0000FFFF" "healthy cortex cell 84" "GSM1657954" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486285" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995944" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657954/GSM1657954_1772078236.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995944" "GSM1657954_1772078236.C61.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 37.0157578159124 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1430295 3953 919100 37.0157578159124 "#0000FFFF" "healthy cortex cell 85" "GSM1657955" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486286" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995945" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657955/GSM1657955_1772078236.C65.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995945" "GSM1657955_1772078236.C65.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 36.8003076780587 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1970772 5141 1203419 36.8003076780587 "#9D0062FF" "healthy cortex cell 86" "GSM1657956" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486287" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995946" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657956/GSM1657956_1772078236.C66.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995946" "GSM1657956_1772078236.C66.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 37.674495507963 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1804119 5377 1156939 37.674495507963 "#90006FFF" "healthy cortex cell 87" "GSM1657957" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486288" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995947" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657957/GSM1657957_1772078236.C70.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995947" "GSM1657957_1772078236.C70.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 36.0072492789477 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1576371 6352 984714 36.0072492789477 "#0000FFFF" "healthy cortex cell 88" "GSM1657958" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486289" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995948" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657958/GSM1657958_1772078236.C74.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995948" "GSM1657958_1772078236.C74.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.9895373387262 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1777080 8117 1223230 35.9895373387262 "#6E0091FF" "healthy cortex cell 89" "GSM1657959" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486290" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995949" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657959/GSM1657959_1772078236.C77.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995949" "GSM1657959_1772078236.C77.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.9277546349913 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1769592 4526 967841 35.9277546349913 "#1400EBFF" "healthy cortex cell 90" "GSM1657960" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486291" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995950" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657960/GSM1657960_1772078236.C89.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995950" "GSM1657960_1772078236.C89.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 35.8650147588924 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1249258 16854 1096226 35.8650147588924 "#0000FFFF" "healthy cortex cell 91" "GSM1657961" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486292" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995951" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657961/GSM1657961_1772078236.C90.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995951" "GSM1657961_1772078236.C90.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 38.1540062623098 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1837449 5067 1437259 38.1540062623098 "#72008DFF" "healthy cortex cell 92" "GSM1657962" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078236" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486293" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995952" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657962/GSM1657962_1772078236.C93.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995952" "GSM1657962_1772078236.C93.csv" "Illumina NextSeq 500" "1772078236" "TemporalLobe" "neurons" 37 37 36.1739690853283 "AB_S11" 4 2 "red" 21 22 2 "#00008BFF" "#0000FFFF" 1118810 9300 799689 36.1739690853283 "#94006BFF" "healthy cortex cell 93" "GSM1657963" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486294" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995953" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657963/GSM1657963_1772078237.C06.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995953" "GSM1657963_1772078237.C06.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 35.2490899013355 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1162651 12907 882065 35.2490899013355 "#A2005DFF" "healthy cortex cell 94" "GSM1657964" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486295" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995954" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657964/GSM1657964_1772078237.C08.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995954" "GSM1657964_1772078237.C08.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 36.6401993567124 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 2448000 6622 1473915 36.6401993567124 "#B80047FF" "healthy cortex cell 95" "GSM1657965" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486236" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995955" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657965/GSM1657965_1772078237.C11.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995955" "GSM1657965_1772078237.C11.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "astrocytes" 37 37 38.5971371307969 "AB_S11" 4 2 "yellow" 22 22 2 "#0000FFFF" "#0000FFFF" 1589134 15321 1379300 38.5971371307969 "#0000FFFF" "healthy cortex cell 96" "GSM1657966" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486237" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995956" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657966/GSM1657966_1772078237.C13.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995956" "GSM1657966_1772078237.C13.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 37.700141645968 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1405862 15855 1325638 37.700141645968 "#1400EBFF" "healthy cortex cell 97" "GSM1657967" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486238" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995957" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657967/GSM1657967_1772078237.C14.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995957" "GSM1657967_1772078237.C14.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 36.8690522126853 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1550713 12608 1251687 36.8690522126853 "#5200ADFF" "healthy cortex cell 98" "GSM1657968" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486239" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995958" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657968/GSM1657968_1772078237.C15.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995958" "GSM1657968_1772078237.C15.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 37.3731092046946 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 3087813 6587 2335355 37.3731092046946 "#6D0092FF" "healthy cortex cell 99" "GSM1657969" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486240" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995959" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657969/GSM1657969_1772078237.C19.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995959" "GSM1657969_1772078237.C19.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "astrocytes" 37 37 35.0054870806634 "AB_S11" 4 2 "yellow" 22 22 2 "#0000FFFF" "#0000FFFF" 1488170 10237 1398929 35.0054870806634 "#0000FFFF" "healthy cortex cell 100" "GSM1657970" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486241" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995960" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657970/GSM1657970_1772078237.C21.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995960" "GSM1657970_1772078237.C21.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 35.4874682147056 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 2304156 3896 1666668 35.4874682147056 "#1F00E0FF" "healthy cortex cell 101" "GSM1657971" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486242" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995961" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657971/GSM1657971_1772078237.C26.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995961" "GSM1657971_1772078237.C26.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 38.9930161256343 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 2749708 16739 2111737 38.9930161256343 "#91006EFF" "healthy cortex cell 102" "GSM1657972" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486243" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995962" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657972/GSM1657972_1772078237.C28.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995962" "GSM1657972_1772078237.C28.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "endothelial" 37 37 36.4882473358884 "AB_S11" 4 2 "springgreen4" 23 22 2 "#0000FFFF" "#0000FFFF" 1072981 15931 1165766 36.4882473358884 "#1400EBFF" "healthy cortex cell 103" "GSM1657973" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486244" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995963" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657973/GSM1657973_1772078237.C29.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995963" "GSM1657973_1772078237.C29.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 37.3167858477682 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 2391913 8422 1582551 37.3167858477682 "#A0005FFF" "healthy cortex cell 104" "GSM1657974" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486245" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995964" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657974/GSM1657974_1772078237.C31.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995964" "GSM1657974_1772078237.C31.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 38.1435487885028 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1439345 9654 2322507 38.1435487885028 "#0000FFFF" "healthy cortex cell 105" "GSM1657975" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486246" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995965" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657975/GSM1657975_1772078237.C40.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995965" "GSM1657975_1772078237.C40.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "astrocytes" 37 37 38.289035120979 "AB_S11" 4 2 "yellow" 22 22 2 "#0000FFFF" "#0000FFFF" 1694764 8299 1189827 38.289035120979 "#0000FFFF" "healthy cortex cell 106" "GSM1657976" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486247" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995966" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657976/GSM1657976_1772078237.C42.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995966" "GSM1657976_1772078237.C42.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 38.4074282487854 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1597472 1625 1409222 38.4074282487854 "#2700D8FF" "healthy cortex cell 107" "GSM1657977" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486248" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995967" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657977/GSM1657977_1772078237.C44.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995967" "GSM1657977_1772078237.C44.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 38.8186613852158 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1984426 14907 1891797 38.8186613852158 "#760089FF" "healthy cortex cell 108" "GSM1657978" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486249" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995968" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657978/GSM1657978_1772078237.C47.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995968" "GSM1657978_1772078237.C47.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 38.0351243894547 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1557750 5821 1420820 38.0351243894547 "#0000FFFF" "healthy cortex cell 109" "GSM1657979" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486250" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995969" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657979/GSM1657979_1772078237.C49.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995969" "GSM1657979_1772078237.C49.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "astrocytes" 37 37 37.6055268254131 "AB_S11" 4 2 "yellow" 22 22 2 "#0000FFFF" "#0000FFFF" 1214075 11887 1108166 37.6055268254131 "#0000FFFF" "healthy cortex cell 110" "GSM1657980" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486251" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995970" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657980/GSM1657980_1772078237.C52.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995970" "GSM1657980_1772078237.C52.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 38.8701892150566 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1693202 11923 1283943 38.8701892150566 "#80007FFF" "healthy cortex cell 111" "GSM1657981" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486252" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995971" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657981/GSM1657981_1772078237.C55.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995971" "GSM1657981_1772078237.C55.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "astrocytes" 37 37 35.7991103436798 "AB_S11" 4 2 "yellow" 22 22 2 "#0000FFFF" "#0000FFFF" 1482709 9547 961824 35.7991103436798 "#0000FFFF" "healthy cortex cell 112" "GSM1657982" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486253" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995972" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657982/GSM1657982_1772078237.C56.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995972" "GSM1657982_1772078237.C56.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 38.9565381379798 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1404519 15214 1355611 38.9565381379798 "#0000FFFF" "healthy cortex cell 113" "GSM1657983" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486254" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995973" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657983/GSM1657983_1772078237.C58.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995973" "GSM1657983_1772078237.C58.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 35.5556620899588 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1900877 5226 1166346 35.5556620899588 "#0000FFFF" "healthy cortex cell 114" "GSM1657984" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486255" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995974" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657984/GSM1657984_1772078237.C60.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995974" "GSM1657984_1772078237.C60.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 35.0460285479203 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1802143 5413 1396189 35.0460285479203 "#5700A8FF" "healthy cortex cell 115" "GSM1657985" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486256" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995975" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657985/GSM1657985_1772078237.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995975" "GSM1657985_1772078237.C61.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 35.668724283576 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 2147345 10101 1802654 35.668724283576 "#0000FFFF" "healthy cortex cell 116" "GSM1657986" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486257" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995976" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657986/GSM1657986_1772078237.C62.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995976" "GSM1657986_1772078237.C62.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 38.150251458399 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1680760 13611 1376528 38.150251458399 "#74008BFF" "healthy cortex cell 117" "GSM1657987" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486258" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995977" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657987/GSM1657987_1772078237.C74.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995977" "GSM1657987_1772078237.C74.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 37.3104490470141 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1709874 13777 1529931 37.3104490470141 "#92006DFF" "healthy cortex cell 118" "GSM1657988" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486259" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995978" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657988/GSM1657988_1772078237.C79.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995978" "GSM1657988_1772078237.C79.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 35.5472442088649 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 2176856 7358 1451138 35.5472442088649 "#3B00C4FF" "healthy cortex cell 119" "GSM1657989" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486260" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995979" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657989/GSM1657989_1772078237.C83.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995979" "GSM1657989_1772078237.C83.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 35.8477552076802 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 2399679 3879 1597686 35.8477552076802 "#5300ACFF" "healthy cortex cell 120" "GSM1657990" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486261" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995980" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657990/GSM1657990_1772078237.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995980" "GSM1657990_1772078237.C84.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 35.1302574248984 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1776419 8725 1309645 35.1302574248984 "#B0004FFF" "healthy cortex cell 121" "GSM1657991" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 37 years" "c1 chip id: 1772078237" "experiment_sample_name: AB_S11" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486262" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995981" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657991/GSM1657991_1772078237.C92.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995981" "GSM1657991_1772078237.C92.csv" "Illumina NextSeq 500" "1772078237" "TemporalLobe" "neurons" 37 37 37.1048912927508 "AB_S11" 4 2 "red" 21 22 2 "#0000FFFF" "#0000FFFF" 1403945 10171 1117582 37.1048912927508 "#770088FF" "healthy cortex cell 122" "GSM1657992" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID12" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486263" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995982" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657992/GSM1657992_nochipID12.C05.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995982" "GSM1657992_nochipID12.C05.csv" "Illumina MiSeq" "nochipID12" "TemporalLobe" "astrocytes" 47 47 47.8237096127123 "AB_S1" 5 2 "yellow" 22 7 1 "#00FF00FF" "#8A2BE2FF" 654124 1272 286673 47.8237096127123 "#0000FFFF" "healthy cortex cell 123" "GSM1657993" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 47 years" "c1 chip id: nochipID12" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486264" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995983" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657993/GSM1657993_nochipID12.C23.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995983" "GSM1657993_nochipID12.C23.csv" "Illumina MiSeq" "nochipID12" "TemporalLobe" "endothelial" 47 47 47.808784974739 "AB_S1" 5 2 "springgreen4" 23 7 1 "#00FF00FF" "#8A2BE2FF" 795155 5802 412076 47.808784974739 "#1400EBFF" "healthy cortex cell 124" "GSM1657994" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 47 years" "c1 chip id: nochipID12" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486265" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995984" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657994/GSM1657994_nochipID12.C73.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995984" "GSM1657994_nochipID12.C73.csv" "Illumina MiSeq" "nochipID12" "TemporalLobe" "microglia" 47 47 45.9773916862905 "AB_S1" 5 2 "springgreen" 7 7 1 "#00FF00FF" "#8A2BE2FF" 957178 5742 576184 45.9773916862905 "#0000FFFF" "healthy cortex cell 125" "GSM1657995" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 47 years" "c1 chip id: nochipID12" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486206" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995985" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657995/GSM1657995_nochipID12.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995985" "GSM1657995_nochipID12.C84.csv" "Illumina MiSeq" "nochipID12" "TemporalLobe" "endothelial" 47 47 45.9659303128719 "AB_S1" 5 2 "springgreen4" 23 7 1 "#00FF00FF" "#8A2BE2FF" 862150 3740 589734 45.9659303128719 "#1400EBFF" "healthy cortex cell 126" "GSM1657996" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 47 years" "c1 chip id: nochipID12" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486207" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995986" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657996/GSM1657996_nochipID12.C87.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995986" "GSM1657996_nochipID12.C87.csv" "Illumina MiSeq" "nochipID12" "TemporalLobe" "microglia" 47 47 45.9884359519929 "AB_S1" 5 2 "springgreen" 7 7 1 "#00FF00FF" "#8A2BE2FF" 660623 6973 457801 45.9884359519929 "#0000FFFF" "healthy cortex cell 127" "GSM1657997" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 63 years" "c1 chip id: nochipID14" "experiment_sample_name: AB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486208" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995987" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657997/GSM1657997_nochipID14.C08.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995987" "GSM1657997_nochipID14.C08.csv" "Illumina MiSeq" "nochipID14" "TemporalLobe" "microglia" 63 63 63.9692178182304 "AB_S2" 3 2 "springgreen" 7 23 1 "#FFFF00FF" "#0000FFFF" 469395 2325 214377 63.9692178182304 "#0000FFFF" "healthy cortex cell 128" "GSM1657998" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 63 years" "c1 chip id: nochipID14" "experiment_sample_name: AB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486209" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995988" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657998/GSM1657998_nochipID14.C13.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995988" "GSM1657998_nochipID14.C13.csv" "Illumina MiSeq" "nochipID14" "TemporalLobe" "astrocytes" 63 63 63.1061795502901 "AB_S2" 3 2 "yellow" 22 23 1 "#FFFF00FF" "#0000FFFF" 712089 2415 354639 63.1061795502901 "#0000FFFF" "healthy cortex cell 129" "GSM1657999" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 63 years" "c1 chip id: nochipID14" "experiment_sample_name: AB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486210" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995989" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1657nnn/GSM1657999/GSM1657999_nochipID14.C29.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995989" "GSM1657999_nochipID14.C29.csv" "Illumina MiSeq" "nochipID14" "TemporalLobe" "microglia" 63 63 62.1771418862045 "AB_S2" 3 2 "springgreen" 7 23 1 "#FFFF00FF" "#0000FFFF" 776276 2846 561846 62.1771418862045 "#1F00E0FF" "healthy cortex cell 130" "GSM1658000" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 63 years" "c1 chip id: nochipID14" "experiment_sample_name: AB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486211" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995990" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658000/GSM1658000_nochipID14.C45.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995990" "GSM1658000_nochipID14.C45.csv" "Illumina MiSeq" "nochipID14" "TemporalLobe" "astrocytes" 63 63 61.4251012103632 "AB_S2" 3 2 "yellow" 22 23 1 "#FFFF00FF" "#0000FFFF" 671769 2221 305196 61.4251012103632 "#1F00E0FF" "healthy cortex cell 131" "GSM1658001" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID14" "experiment_sample_name: AB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486212" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995991" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658001/GSM1658001_nochipID14.C89.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995991" "GSM1658001_nochipID14.C89.csv" "Illumina MiSeq" "nochipID14" "TemporalLobe" "neurons" 63 63 63.934169231914 "AB_S2" 3 2 "red" 21 23 1 "#FFFF00FF" "#0000FFFF" 767096 1292 369897 63.934169231914 "#8C0073FF" "healthy cortex cell 132" "GSM1658002" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 22 years" "c1 chip id: nochipID15" "experiment_sample_name: AB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486213" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995992" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658002/GSM1658002_nochipID15.C20.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995992" "GSM1658002_nochipID15.C20.csv" "Illumina MiSeq" "nochipID15" "TemporalLobe" "neurons" 22 22 21.0755550824106 "AB_S3" 6 2 "red" 21 4 1 "#FFA500FF" "#00FF00FF" 1455476 8298 578048 21.0755550824106 "#9A0065FF" "healthy cortex cell 133" "GSM1658003" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: postnatal 22 years" "c1 chip id: nochipID15" "experiment_sample_name: AB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486214" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995993" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658003/GSM1658003_nochipID15.C54.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995993" "GSM1658003_nochipID15.C54.csv" "Illumina MiSeq" "nochipID15" "TemporalLobe" "fetalQui" 22 22 22.1895774072036 "AB_S3" 6 2 "orange" 4 4 1 "#FFA500FF" "#00FF00FF" 1138213 4035 438651 22.1895774072036 "#D70028FF" "healthy cortex cell 134" "GSM1658004" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 22 years" "c1 chip id: nochipID15" "experiment_sample_name: AB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486215" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995994" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658004/GSM1658004_nochipID15.C69.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995994" "GSM1658004_nochipID15.C69.csv" "Illumina MiSeq" "nochipID15" "TemporalLobe" "endothelial" 22 22 20.7100955629721 "AB_S3" 6 2 "springgreen4" 23 4 1 "#FFA500FF" "#00FF00FF" 1023601 5727 474330 20.7100955629721 "#0000FFFF" "healthy cortex cell 135" "GSM1658005" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 22 years" "c1 chip id: nochipID15" "experiment_sample_name: AB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486216" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995995" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658005/GSM1658005_nochipID15.C86.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995995" "GSM1658005_nochipID15.C86.csv" "Illumina MiSeq" "nochipID15" "TemporalLobe" "neurons" 22 22 20.3011095402762 "AB_S3" 6 2 "red" 21 4 1 "#FFA500FF" "#00FF00FF" 1011528 3662 374062 20.3011095402762 "#890076FF" "healthy cortex cell 136" "GSM1658006" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486217" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995996" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658006/GSM1658006_nochipID2.C01.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995996" "GSM1658006_nochipID2.C01.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 49.4806117573753 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2044854 17452 554150 49.4806117573753 "#0000FFFF" "healthy cortex cell 137" "GSM1658007" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486218" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995997" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658007/GSM1658007_nochipID2.C02.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995997" "GSM1658007_nochipID2.C02.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.3973617823794 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2245424 9547 477299 51.3973617823794 "#0000FFFF" "healthy cortex cell 138" "GSM1658008" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486219" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995998" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658008/GSM1658008_nochipID2.C03.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995998" "GSM1658008_nochipID2.C03.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 48.661247628741 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 1181279 9676 360066 48.661247628741 "#A1005EFF" "healthy cortex cell 139" "GSM1658009" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486220" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX995999" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658009/GSM1658009_nochipID2.C07.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995999" "GSM1658009_nochipID2.C07.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 49.6352251395583 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 1692193 18343 499024 49.6352251395583 "#D3002CFF" "healthy cortex cell 140" "GSM1658010" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486221" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996000" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658010/GSM1658010_nochipID2.C08.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996000" "GSM1658010_nochipID2.C08.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.4498929446563 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2241263 7871 523194 51.4498929446563 "#4800B7FF" "healthy cortex cell 141" "GSM1658011" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486222" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996001" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658011/GSM1658011_nochipID2.C09.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996001" "GSM1658011_nochipID2.C09.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 51.9206880955026 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2419279 15855 592892 51.9206880955026 "#C80037FF" "healthy cortex cell 142" "GSM1658012" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486223" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996002" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658012/GSM1658012_nochipID2.C10.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996002" "GSM1658012_nochipID2.C10.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 48.9922788701952 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 970576 5474 208928 48.9922788701952 "#93006CFF" "healthy cortex cell 143" "GSM1658013" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486224" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996003" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658013/GSM1658013_nochipID2.C11.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996003" "GSM1658013_nochipID2.C11.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 49.3691666126251 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 3150057 14171 713105 49.3691666126251 "#CD0032FF" "healthy cortex cell 144" "GSM1658014" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486225" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996004" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658014/GSM1658014_nochipID2.C12.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996004" "GSM1658014_nochipID2.C12.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 51.2032004455104 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 3098378 25499 879852 51.2032004455104 "#AC0053FF" "healthy cortex cell 145" "GSM1658015" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486226" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996005" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658015/GSM1658015_nochipID2.C13.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996005" "GSM1658015_nochipID2.C13.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 48.5093739330769 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2272103 12823 519490 48.5093739330769 "#6C0093FF" "healthy cortex cell 146" "GSM1658016" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486227" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996006" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658016/GSM1658016_nochipID2.C14.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996006" "GSM1658016_nochipID2.C14.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.5695007340983 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1753565 9206 407037 50.5695007340983 "#0000FFFF" "healthy cortex cell 147" "GSM1658017" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486228" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996007" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658017/GSM1658017_nochipID2.C15.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996007" "GSM1658017_nochipID2.C15.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.7838198691607 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1239031 5986 319667 48.7838198691607 "#0000FFFF" "healthy cortex cell 148" "GSM1658018" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486229" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996008" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658018/GSM1658018_nochipID2.C16.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996008" "GSM1658018_nochipID2.C16.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "oligodendrocytes" 50 50 49.4762677084655 "AB_S4" 7 2 "dodgerblue" 24 10 2 "#FFA500FF" "#00FF00FF" 2516767 13635 803548 49.4762677084655 "#0000FFFF" "healthy cortex cell 149" "GSM1658019" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486230" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996009" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658019/GSM1658019_nochipID2.C17.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996009" "GSM1658019_nochipID2.C17.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 51.1278889682144 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2911604 21937 743414 51.1278889682144 "#9F0060FF" "healthy cortex cell 150" "GSM1658020" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486231" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996010" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658020/GSM1658020_nochipID2.C18.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996010" "GSM1658020_nochipID2.C18.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.940154530108 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2954430 12199 711008 51.940154530108 "#0000FFFF" "healthy cortex cell 151" "GSM1658021" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486232" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996011" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658021/GSM1658021_nochipID2.C19.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996011" "GSM1658021_nochipID2.C19.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.1950305756181 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1860653 7427 404040 51.1950305756181 "#0000FFFF" "healthy cortex cell 152" "GSM1658022" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486233" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996012" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658022/GSM1658022_nochipID2.C21.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996012" "GSM1658022_nochipID2.C21.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 50.697925596498 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 1328366 7963 294703 50.697925596498 "#B80047FF" "healthy cortex cell 153" "GSM1658023" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486234" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996013" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658023/GSM1658023_nochipID2.C22.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996013" "GSM1658023_nochipID2.C22.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 48.4213414862752 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2078663 4282 690428 48.4213414862752 "#3700C8FF" "healthy cortex cell 154" "GSM1658024" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486235" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996014" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658024/GSM1658024_nochipID2.C24.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996014" "GSM1658024_nochipID2.C24.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 51.7567779812962 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 1896601 5145 486227 51.7567779812962 "#63009CFF" "healthy cortex cell 155" "GSM1658025" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486176" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996015" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658025/GSM1658025_nochipID2.C26.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996015" "GSM1658025_nochipID2.C26.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 49.0015122452751 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 3521114 6121 708556 49.0015122452751 "#BA0045FF" "healthy cortex cell 156" "GSM1658026" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486177" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996016" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658026/GSM1658026_nochipID2.C27.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996016" "GSM1658026_nochipID2.C27.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.3083161823452 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2098698 7610 494827 48.3083161823452 "#0000FFFF" "healthy cortex cell 157" "GSM1658027" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486178" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996017" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658027/GSM1658027_nochipID2.C28.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996017" "GSM1658027_nochipID2.C28.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 49.7235200600699 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2103202 5928 427979 49.7235200600699 "#0000FFFF" "healthy cortex cell 158" "GSM1658028" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486179" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996018" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658028/GSM1658028_nochipID2.C29.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996018" "GSM1658028_nochipID2.C29.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 50.2224575774744 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2150265 16220 597959 50.2224575774744 "#8B0074FF" "healthy cortex cell 159" "GSM1658029" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486180" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996019" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658029/GSM1658029_nochipID2.C30.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996019" "GSM1658029_nochipID2.C30.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.5723138712347 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2358262 13883 603661 50.5723138712347 "#0000FFFF" "healthy cortex cell 160" "GSM1658030" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486181" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996020" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658030/GSM1658030_nochipID2.C31.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996020" "GSM1658030_nochipID2.C31.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 51.9577633179724 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 342678 17373 488358 51.9577633179724 "#5A00A5FF" "healthy cortex cell 161" "GSM1658031" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486182" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996021" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658031/GSM1658031_nochipID2.C32.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996021" "GSM1658031_nochipID2.C32.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.8156666774303 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2031830 8878 505497 50.8156666774303 "#0000FFFF" "healthy cortex cell 162" "GSM1658032" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486183" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996022" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658032/GSM1658032_nochipID2.C33.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996022" "GSM1658032_nochipID2.C33.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 51.3189040319994 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2891439 15360 662477 51.3189040319994 "#4400BBFF" "healthy cortex cell 163" "GSM1658033" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486184" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996023" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658033/GSM1658033_nochipID2.C34.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996023" "GSM1658033_nochipID2.C34.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 51.1375270178542 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2393614 17205 692021 51.1375270178542 "#B80047FF" "healthy cortex cell 164" "GSM1658034" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486185" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996024" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658034/GSM1658034_nochipID2.C36.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996024" "GSM1658034_nochipID2.C36.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 48.2328145382926 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 3923864 17859 958869 48.2328145382926 "#B70048FF" "healthy cortex cell 165" "GSM1658035" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486186" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996025" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658035/GSM1658035_nochipID2.C38.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996025" "GSM1658035_nochipID2.C38.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 50.9567773696035 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2046270 4872 519591 50.9567773696035 "#1400EBFF" "healthy cortex cell 166" "GSM1658036" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486187" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996026" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658036/GSM1658036_nochipID2.C39.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996026" "GSM1658036_nochipID2.C39.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 49.9046526458114 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2414289 3455 633928 49.9046526458114 "#0000FFFF" "healthy cortex cell 167" "GSM1658037" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486188" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996027" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658037/GSM1658037_nochipID2.C40.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996027" "GSM1658037_nochipID2.C40.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 51.3556417003274 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2614536 22363 854482 51.3556417003274 "#BD0042FF" "healthy cortex cell 168" "GSM1658038" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486189" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996028" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658038/GSM1658038_nochipID2.C41.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996028" "GSM1658038_nochipID2.C41.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 48.3688235878944 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2097362 3278 562705 48.3688235878944 "#0000FFFF" "healthy cortex cell 169" "GSM1658039" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486190" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996029" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658039/GSM1658039_nochipID2.C42.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996029" "GSM1658039_nochipID2.C42.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 48.1094246581197 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 1650250 8375 513213 48.1094246581197 "#0000FFFF" "healthy cortex cell 170" "GSM1658040" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486191" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996030" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658040/GSM1658040_nochipID2.C43.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996030" "GSM1658040_nochipID2.C43.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 50.7602716060355 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2034883 13226 442382 50.7602716060355 "#0000FFFF" "healthy cortex cell 171" "GSM1658041" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486192" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996031" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658041/GSM1658041_nochipID2.C44.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996031" "GSM1658041_nochipID2.C44.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 50.6713692964986 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 1404744 17896 487236 50.6713692964986 "#0000FFFF" "healthy cortex cell 172" "GSM1658042" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486193" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996032" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658042/GSM1658042_nochipID2.C45.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996032" "GSM1658042_nochipID2.C45.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 50.2580025857314 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2680358 4273 564437 50.2580025857314 "#1F00E0FF" "healthy cortex cell 173" "GSM1658043" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486194" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996033" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658043/GSM1658043_nochipID2.C46.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996033" "GSM1658043_nochipID2.C46.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.1843312438577 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2452707 21333 673170 48.1843312438577 "#0000FFFF" "healthy cortex cell 174" "GSM1658044" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486195" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996034" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658044/GSM1658044_nochipID2.C47.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996034" "GSM1658044_nochipID2.C47.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 48.9064798997715 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2118984 5764 509914 48.9064798997715 "#3B00C4FF" "healthy cortex cell 175" "GSM1658045" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486196" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996035" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658045/GSM1658045_nochipID2.C48.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996035" "GSM1658045_nochipID2.C48.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.6602360950783 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2164997 6184 626853 48.6602360950783 "#0000FFFF" "healthy cortex cell 176" "GSM1658046" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486197" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996036" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658046/GSM1658046_nochipID2.C49.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996036" "GSM1658046_nochipID2.C49.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 48.7051684772596 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2117819 4708 379879 48.7051684772596 "#690096FF" "healthy cortex cell 177" "GSM1658047" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486198" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996037" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658047/GSM1658047_nochipID2.C50.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996037" "GSM1658047_nochipID2.C50.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 51.9981933217496 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2054428 10972 557530 51.9981933217496 "#9E0061FF" "healthy cortex cell 178" "GSM1658048" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486199" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996038" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658048/GSM1658048_nochipID2.C51.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996038" "GSM1658048_nochipID2.C51.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.6745037939399 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1828172 4484 338858 51.6745037939399 "#0000FFFF" "healthy cortex cell 179" "GSM1658049" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486200" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996039" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658049/GSM1658049_nochipID2.C52.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996039" "GSM1658049_nochipID2.C52.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.4338354198262 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1648681 4018 428041 48.4338354198262 "#0000FFFF" "healthy cortex cell 180" "GSM1658050" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486201" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996040" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658050/GSM1658050_nochipID2.C56.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996040" "GSM1658050_nochipID2.C56.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.9707082305104 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2190399 12459 644679 50.9707082305104 "#0000FFFF" "healthy cortex cell 181" "GSM1658051" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486202" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996041" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658051/GSM1658051_nochipID2.C57.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996041" "GSM1658051_nochipID2.C57.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.8116374900565 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2689735 10698 590436 50.8116374900565 "#0000FFFF" "healthy cortex cell 182" "GSM1658052" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486203" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996042" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658052/GSM1658052_nochipID2.C58.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996042" "GSM1658052_nochipID2.C58.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 49.4506490146741 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2620059 14288 551392 49.4506490146741 "#B5004AFF" "healthy cortex cell 183" "GSM1658053" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486204" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996043" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658053/GSM1658053_nochipID2.C59.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996043" "GSM1658053_nochipID2.C59.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.3785348972306 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2060298 8688 492863 50.3785348972306 "#0000FFFF" "healthy cortex cell 184" "GSM1658054" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486205" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996044" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658054/GSM1658054_nochipID2.C60.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996044" "GSM1658054_nochipID2.C60.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.4584476640448 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1675527 8001 397652 51.4584476640448 "#0000FFFF" "healthy cortex cell 185" "GSM1658055" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486146" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996045" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658055/GSM1658055_nochipID2.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996045" "GSM1658055_nochipID2.C61.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.0638598054647 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1074528 3351 426749 51.0638598054647 "#0000FFFF" "healthy cortex cell 186" "GSM1658056" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486147" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996046" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658056/GSM1658056_nochipID2.C62.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996046" "GSM1658056_nochipID2.C62.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.368351040408 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2523236 7974 578488 48.368351040408 "#0000FFFF" "healthy cortex cell 187" "GSM1658057" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486148" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996047" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658057/GSM1658057_nochipID2.C63.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996047" "GSM1658057_nochipID2.C63.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 49.7378604719415 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2423534 18656 563527 49.7378604719415 "#B1004EFF" "healthy cortex cell 188" "GSM1658058" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486149" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996048" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658058/GSM1658058_nochipID2.C64.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996048" "GSM1658058_nochipID2.C64.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 48.25684638042 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 3389068 10968 578624 48.25684638042 "#BE0041FF" "healthy cortex cell 189" "GSM1658059" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486150" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996049" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658059/GSM1658059_nochipID2.C65.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996049" "GSM1658059_nochipID2.C65.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 49.4572679521516 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2771359 13160 558822 49.4572679521516 "#0000FFFF" "healthy cortex cell 190" "GSM1658060" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486151" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996050" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658060/GSM1658060_nochipID2.C66.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996050" "GSM1658060_nochipID2.C66.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.9852039813995 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 3451169 10176 803566 48.9852039813995 "#0000FFFF" "healthy cortex cell 191" "GSM1658061" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486152" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996051" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658061/GSM1658061_nochipID2.C67.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996051" "GSM1658061_nochipID2.C67.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.8764298288152 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2220475 7142 389514 50.8764298288152 "#0000FFFF" "healthy cortex cell 192" "GSM1658062" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486153" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996052" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658062/GSM1658062_nochipID2.C68.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996052" "GSM1658062_nochipID2.C68.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 49.7760759051889 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1420153 6945 410285 49.7760759051889 "#0000FFFF" "healthy cortex cell 193" "GSM1658063" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486154" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996053" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658063/GSM1658063_nochipID2.C69.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996053" "GSM1658063_nochipID2.C69.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 48.5748846735805 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 2251897 14257 513582 48.5748846735805 "#0000FFFF" "healthy cortex cell 194" "GSM1658064" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486155" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996054" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658064/GSM1658064_nochipID2.C71.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996054" "GSM1658064_nochipID2.C71.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.7901773955673 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1423370 7936 297310 48.7901773955673 "#0000FFFF" "healthy cortex cell 195" "GSM1658065" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486156" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996055" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658065/GSM1658065_nochipID2.C73.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996055" "GSM1658065_nochipID2.C73.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.4693666249514 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1679892 12172 552492 48.4693666249514 "#0000FFFF" "healthy cortex cell 196" "GSM1658066" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486157" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996056" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658066/GSM1658066_nochipID2.C75.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996056" "GSM1658066_nochipID2.C75.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.8865847699344 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1435689 4503 384183 50.8865847699344 "#0000FFFF" "healthy cortex cell 197" "GSM1658067" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486158" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996057" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658067/GSM1658067_nochipID2.C76.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996057" "GSM1658067_nochipID2.C76.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 49.5029242895544 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2781033 9028 571995 49.5029242895544 "#0000FFFF" "healthy cortex cell 198" "GSM1658068" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486159" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996058" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658068/GSM1658068_nochipID2.C77.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996058" "GSM1658068_nochipID2.C77.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.4778029192239 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2049257 6073 396459 51.4778029192239 "#0000FFFF" "healthy cortex cell 199" "GSM1658069" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486160" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996059" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658069/GSM1658069_nochipID2.C78.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996059" "GSM1658069_nochipID2.C78.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.2257988788188 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1948475 11868 535814 50.2257988788188 "#0000FFFF" "healthy cortex cell 200" "GSM1658070" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486161" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996060" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658070/GSM1658070_nochipID2.C79.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996060" "GSM1658070_nochipID2.C79.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 51.4387538479641 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 1935393 20781 624256 51.4387538479641 "#85007AFF" "healthy cortex cell 201" "GSM1658071" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486162" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996061" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658071/GSM1658071_nochipID2.C80.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996061" "GSM1658071_nochipID2.C80.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.2983691655099 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2596020 15528 637892 48.2983691655099 "#0000FFFF" "healthy cortex cell 202" "GSM1658072" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486163" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996062" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658072/GSM1658072_nochipID2.C81.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996062" "GSM1658072_nochipID2.C81.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 51.0091225365177 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1606851 13100 493683 51.0091225365177 "#0000FFFF" "healthy cortex cell 203" "GSM1658073" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486164" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996063" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658073/GSM1658073_nochipID2.C82.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996063" "GSM1658073_nochipID2.C82.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 50.2757164053619 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2741131 14919 646361 50.2757164053619 "#0000FFFF" "healthy cortex cell 204" "GSM1658074" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486165" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996064" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658074/GSM1658074_nochipID2.C83.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996064" "GSM1658074_nochipID2.C83.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 51.1188255771995 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2870804 26208 788395 51.1188255771995 "#B3004CFF" "healthy cortex cell 205" "GSM1658075" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486168" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996065" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658075/GSM1658075_nochipID2.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996065" "GSM1658075_nochipID2.C84.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 50.8223128477111 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2925926 14801 675127 50.8223128477111 "#C60039FF" "healthy cortex cell 206" "GSM1658076" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486169" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996066" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658076/GSM1658076_nochipID2.C85.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996066" "GSM1658076_nochipID2.C85.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 49.7243474507704 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2532147 9312 615771 49.7243474507704 "#71008EFF" "healthy cortex cell 207" "GSM1658077" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486170" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996067" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658077/GSM1658077_nochipID2.C86.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996067" "GSM1658077_nochipID2.C86.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "hybrid" 50 50 50.717539283447 "AB_S4" 7 2 "deeppink" 9 10 2 "#FFA500FF" "#00FF00FF" 2932768 8908 875398 50.717539283447 "#0000FFFF" "healthy cortex cell 208" "GSM1658078" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486171" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996068" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658078/GSM1658078_nochipID2.C87.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996068" "GSM1658078_nochipID2.C87.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 49.67174474895 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 1138331 10968 274724 49.67174474895 "#0000FFFF" "healthy cortex cell 209" "GSM1658079" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486172" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996069" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658079/GSM1658079_nochipID2.C89.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996069" "GSM1658079_nochipID2.C89.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 48.4852066636086 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2798221 13311 646527 48.4852066636086 "#0000FFFF" "healthy cortex cell 210" "GSM1658080" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486173" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996070" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658080/GSM1658080_nochipID2.C90.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996070" "GSM1658080_nochipID2.C90.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "neurons" 50 50 48.9032871574163 "AB_S4" 7 2 "red" 21 10 2 "#FFA500FF" "#00FF00FF" 3047290 17156 746568 48.9032871574163 "#C0003FFF" "healthy cortex cell 211" "GSM1658081" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486166" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996071" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658081/GSM1658081_nochipID2.C92.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996071" "GSM1658081_nochipID2.C92.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 49.7391649084166 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 552489 7608 381098 49.7391649084166 "#5300ACFF" "healthy cortex cell 212" "GSM1658082" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 50 years" "c1 chip id: nochipID2" "experiment_sample_name: AB_S4" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486167" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996072" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658082/GSM1658082_nochipID2.C93.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996072" "GSM1658082_nochipID2.C93.csv" "Illumina NextSeq 500" "nochipID2" "TemporalLobe" "astrocytes" 50 50 49.9331924198195 "AB_S4" 7 2 "yellow" 22 10 2 "#FFA500FF" "#00FF00FF" 2064448 22618 643964 49.9331924198195 "#0000FFFF" "healthy cortex cell 213" "GSM1658083" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486174" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996073" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658083/GSM1658083_nochipID3.C01.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996073" "GSM1658083_nochipID3.C01.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 64.7882555881515 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 729937 3550 766736 64.7882555881515 "#0000FFFF" "healthy cortex cell 214" "GSM1658084" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486175" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996074" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658084/GSM1658084_nochipID3.C05.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996074" "GSM1658084_nochipID3.C05.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 61.2959539731964 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 707004 4193 459981 61.2959539731964 "#0000FFFF" "healthy cortex cell 215" "GSM1658085" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486116" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996075" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658085/GSM1658085_nochipID3.C06.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996075" "GSM1658085_nochipID3.C06.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 61.6048514973372 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 367178 8172 393503 61.6048514973372 "#0000FFFF" "healthy cortex cell 216" "GSM1658086" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486117" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996076" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658086/GSM1658086_nochipID3.C07.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996076" "GSM1658086_nochipID3.C07.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 63.664423099719 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 521207 1860 423609 63.664423099719 "#0000FFFF" "healthy cortex cell 217" "GSM1658087" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486118" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996077" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658087/GSM1658087_nochipID3.C09.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996077" "GSM1658087_nochipID3.C09.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 63.7346561802551 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 791009 4820 506028 63.7346561802551 "#5500AAFF" "healthy cortex cell 218" "GSM1658088" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486119" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996078" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658088/GSM1658088_nochipID3.C11.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996078" "GSM1658088_nochipID3.C11.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "oligodendrocytes" 63 63 62.4239535201341 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#FF0000FF" "#FFFF00FF" 671453 6210 641120 62.4239535201341 "#0000FFFF" "healthy cortex cell 219" "GSM1658089" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486120" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996079" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658089/GSM1658089_nochipID3.C12.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996079" "GSM1658089_nochipID3.C12.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 61.6981576364487 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 591208 2605 547186 61.6981576364487 "#0000FFFF" "healthy cortex cell 220" "GSM1658090" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486121" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996080" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658090/GSM1658090_nochipID3.C14.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996080" "GSM1658090_nochipID3.C14.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 64.0576269356534 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 467269 9609 470071 64.0576269356534 "#AF0050FF" "healthy cortex cell 221" "GSM1658091" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486122" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996081" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658091/GSM1658091_nochipID3.C23.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996081" "GSM1658091_nochipID3.C23.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 61.405024192296 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 791525 5655 539000 61.405024192296 "#1400EBFF" "healthy cortex cell 222" "GSM1658092" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486123" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996082" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658092/GSM1658092_nochipID3.C25.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996082" "GSM1658092_nochipID3.C25.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 63.2502608681098 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 799802 8322 714112 63.2502608681098 "#0000FFFF" "healthy cortex cell 223" "GSM1658093" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486124" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996083" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658093/GSM1658093_nochipID3.C32.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996083" "GSM1658093_nochipID3.C32.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "oligodendrocytes" 63 63 61.3977573951706 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#FF0000FF" "#FFFF00FF" 746539 4927 559261 61.3977573951706 "#0000FFFF" "healthy cortex cell 224" "GSM1658094" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486125" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996084" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658094/GSM1658094_nochipID3.C37.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996084" "GSM1658094_nochipID3.C37.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 62.6885283850133 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 749147 5562 731454 62.6885283850133 "#0000FFFF" "healthy cortex cell 225" "GSM1658095" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486126" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996085" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658095/GSM1658095_nochipID3.C38.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996085" "GSM1658095_nochipID3.C38.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 62.5512959463522 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 618295 5388 577445 62.5512959463522 "#5700A8FF" "healthy cortex cell 226" "GSM1658096" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486127" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996086" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658096/GSM1658096_nochipID3.C51.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996086" "GSM1658096_nochipID3.C51.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 63.4870537817478 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 358694 6666 680393 63.4870537817478 "#0000FFFF" "healthy cortex cell 227" "GSM1658097" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486128" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996087" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658097/GSM1658097_nochipID3.C52.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996087" "GSM1658097_nochipID3.C52.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "oligodendrocytes" 63 63 61.6271655363962 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#FF0000FF" "#FFFF00FF" 1011852 7358 687603 61.6271655363962 "#0000FFFF" "healthy cortex cell 228" "GSM1658098" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486129" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996088" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658098/GSM1658098_nochipID3.C53.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996088" "GSM1658098_nochipID3.C53.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 61.088331126608 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 341021 4153 535075 61.088331126608 "#0000FFFF" "healthy cortex cell 229" "GSM1658099" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486130" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996089" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658099/GSM1658099_nochipID3.C54.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996089" "GSM1658099_nochipID3.C54.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 62.2452983008698 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 559825 2789 423893 62.2452983008698 "#0000FFFF" "healthy cortex cell 230" "GSM1658100" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486131" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996090" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658100/GSM1658100_nochipID3.C56.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996090" "GSM1658100_nochipID3.C56.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 64.9454100234434 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 823836 5012 666859 64.9454100234434 "#6E0091FF" "healthy cortex cell 231" "GSM1658101" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486132" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996091" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658101/GSM1658101_nochipID3.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996091" "GSM1658101_nochipID3.C61.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 64.6064162394032 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 594662 6123 546666 64.6064162394032 "#1400EBFF" "healthy cortex cell 232" "GSM1658102" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486133" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996092" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658102/GSM1658102_nochipID3.C62.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996092" "GSM1658102_nochipID3.C62.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 64.3154003918171 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 576768 6646 559720 64.3154003918171 "#0000FFFF" "healthy cortex cell 233" "GSM1658103" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486134" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996093" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658103/GSM1658103_nochipID3.C65.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996093" "GSM1658103_nochipID3.C65.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 61.9113597059622 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 684089 5973 463364 61.9113597059622 "#5F00A0FF" "healthy cortex cell 234" "GSM1658104" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486135" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996094" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658104/GSM1658104_nochipID3.C69.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996094" "GSM1658104_nochipID3.C69.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 64.1464623566717 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 529132 5893 485532 64.1464623566717 "#0000FFFF" "healthy cortex cell 235" "GSM1658105" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486136" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996095" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658105/GSM1658105_nochipID3.C71.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996095" "GSM1658105_nochipID3.C71.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 61.5235063796863 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 552845 8887 547311 61.5235063796863 "#C0003FFF" "healthy cortex cell 236" "GSM1658106" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486137" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996096" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658106/GSM1658106_nochipID3.C72.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996096" "GSM1658106_nochipID3.C72.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 62.4088985361159 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 821159 9110 673694 62.4088985361159 "#0000FFFF" "healthy cortex cell 237" "GSM1658107" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486138" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996097" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658107/GSM1658107_nochipID3.C74.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996097" "GSM1658107_nochipID3.C74.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 62.3304658886045 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 604681 7644 427438 62.3304658886045 "#780087FF" "healthy cortex cell 238" "GSM1658108" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486139" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996098" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658108/GSM1658108_nochipID3.C75.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996098" "GSM1658108_nochipID3.C75.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 63.3414342775941 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 475801 4392 449218 63.3414342775941 "#0000FFFF" "healthy cortex cell 239" "GSM1658109" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486140" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996099" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658109/GSM1658109_nochipID3.C76.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996099" "GSM1658109_nochipID3.C76.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 61.9325725510716 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 412375 4516 407668 61.9325725510716 "#0000FFFF" "healthy cortex cell 240" "GSM1658110" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486141" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996100" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658110/GSM1658110_nochipID3.C80.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996100" "GSM1658110_nochipID3.C80.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 63.53976125177 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 719416 5386 658370 63.53976125177 "#770088FF" "healthy cortex cell 241" "GSM1658111" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486142" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996101" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658111/GSM1658111_nochipID3.C81.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996101" "GSM1658111_nochipID3.C81.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 64.3226694026962 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 616657 7243 575968 64.3226694026962 "#1F00E0FF" "healthy cortex cell 242" "GSM1658112" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486143" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996102" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658112/GSM1658112_nochipID3.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996102" "GSM1658112_nochipID3.C84.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "endothelial" 63 63 64.3687735861167 "AB_S5" 3 2 "springgreen4" 23 23 2 "#FF0000FF" "#FFFF00FF" 574005 4968 454276 64.3687735861167 "#0000FFFF" "healthy cortex cell 243" "GSM1658113" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486144" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996103" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658113/GSM1658113_nochipID3.C85.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996103" "GSM1658113_nochipID3.C85.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 62.1665315879509 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 733292 6661 610610 62.1665315879509 "#0000FFFF" "healthy cortex cell 244" "GSM1658114" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486145" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996104" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658114/GSM1658114_nochipID3.C86.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996104" "GSM1658114_nochipID3.C86.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 63.6145864268765 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 901570 4692 584089 63.6145864268765 "#1400EBFF" "healthy cortex cell 245" "GSM1658115" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID3" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486086" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996105" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658115/GSM1658115_nochipID3.C91.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996105" "GSM1658115_nochipID3.C91.csv" "Illumina NextSeq 500" "nochipID3" "TemporalLobe" "neurons" 63 63 61.735702816397 "AB_S5" 3 2 "red" 21 23 2 "#FF0000FF" "#FFFF00FF" 667012 5129 632914 61.735702816397 "#970068FF" "healthy cortex cell 246" "GSM1658116" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486087" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996106" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658116/GSM1658116_nochipID5.C04.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996106" "GSM1658116_nochipID5.C04.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "microglia" 63 63 63.1067100809887 "AB_S5" 3 2 "springgreen" 7 23 2 "#8B1A1AFF" "#FFFF00FF" 444442 1577 662487 63.1067100809887 "#0000FFFF" "healthy cortex cell 247" "GSM1658117" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486088" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996107" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658117/GSM1658117_nochipID5.C05.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996107" "GSM1658117_nochipID5.C05.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "endothelial" 63 63 62.1153698470443 "AB_S5" 3 2 "springgreen4" 23 23 2 "#8B1A1AFF" "#FFFF00FF" 569219 1870 471507 62.1153698470443 "#0000FFFF" "healthy cortex cell 248" "GSM1658118" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486089" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996108" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658118/GSM1658118_nochipID5.C18.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996108" "GSM1658118_nochipID5.C18.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "oligodendrocytes" 63 63 64.1067732889205 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#8B1A1AFF" "#FFFF00FF" 668301 5369 481467 64.1067732889205 "#0000FFFF" "healthy cortex cell 249" "GSM1658119" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486090" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996109" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658119/GSM1658119_nochipID5.C19.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996109" "GSM1658119_nochipID5.C19.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "oligodendrocytes" 63 63 61.9568707942963 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#8B1A1AFF" "#FFFF00FF" 285834 13283 419157 61.9568707942963 "#0000FFFF" "healthy cortex cell 250" "GSM1658120" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486091" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996110" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658120/GSM1658120_nochipID5.C42.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996110" "GSM1658120_nochipID5.C42.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "oligodendrocytes" 63 63 61.52800815925 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#8B1A1AFF" "#FFFF00FF" 858316 4819 579305 61.52800815925 "#0000FFFF" "healthy cortex cell 251" "GSM1658121" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486092" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996111" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658121/GSM1658121_nochipID5.C44.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996111" "GSM1658121_nochipID5.C44.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "neurons" 63 63 62.5042795687914 "AB_S5" 3 2 "red" 21 23 2 "#8B1A1AFF" "#FFFF00FF" 448222 3464 341161 62.5042795687914 "#3700C8FF" "healthy cortex cell 252" "GSM1658122" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486093" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996112" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658122/GSM1658122_nochipID5.C45.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996112" "GSM1658122_nochipID5.C45.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "endothelial" 63 63 64.9524675933644 "AB_S5" 3 2 "springgreen4" 23 23 2 "#8B1A1AFF" "#FFFF00FF" 472409 1274 291520 64.9524675933644 "#0000FFFF" "healthy cortex cell 253" "GSM1658123" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486094" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996113" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658123/GSM1658123_nochipID5.C54.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996113" "GSM1658123_nochipID5.C54.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "oligodendrocytes" 63 63 64.4304479630664 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#8B1A1AFF" "#FFFF00FF" 202152 4950 240214 64.4304479630664 "#0000FFFF" "healthy cortex cell 254" "GSM1658124" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486095" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996114" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658124/GSM1658124_nochipID5.C65.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996114" "GSM1658124_nochipID5.C65.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "oligodendrocytes" 63 63 64.130892415531 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#8B1A1AFF" "#FFFF00FF" 716217 6353 553315 64.130892415531 "#0000FFFF" "healthy cortex cell 255" "GSM1658125" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486096" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996115" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658125/GSM1658125_nochipID5.C72.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996115" "GSM1658125_nochipID5.C72.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "oligodendrocytes" 63 63 62.463076332584 "AB_S5" 3 2 "dodgerblue" 24 23 2 "#8B1A1AFF" "#FFFF00FF" 689474 3187 418943 62.463076332584 "#0000FFFF" "healthy cortex cell 256" "GSM1658126" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: endothelial" "age: postnatal 63 years" "c1 chip id: nochipID5" "experiment_sample_name: AB_S5" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486097" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996116" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658126/GSM1658126_nochipID5.C91.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996116" "GSM1658126_nochipID5.C91.csv" "Illumina NextSeq 500" "nochipID5" "TemporalLobe" "endothelial" 63 63 62.3755609961227 "AB_S5" 3 2 "springgreen4" 23 23 2 "#8B1A1AFF" "#FFFF00FF" 654192 3635 426205 62.3755609961227 "#0000FFFF" "healthy cortex cell 257" "GSM1658127" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486098" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996117" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658127/GSM1658127_nochipID8.C01.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996117" "GSM1658127_nochipID8.C01.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 22.9901603702456 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 729965 10014 558787 22.9901603702456 "#7E0081FF" "healthy cortex cell 258" "GSM1658128" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486099" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996118" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658128/GSM1658128_nochipID8.C02.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996118" "GSM1658128_nochipID8.C02.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.0615377528593 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 370112 7947 549829 21.0615377528593 "#0000FFFF" "healthy cortex cell 259" "GSM1658129" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486100" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996119" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658129/GSM1658129_nochipID8.C05.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996119" "GSM1658129_nochipID8.C05.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.1323237400502 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1631898 11181 958717 20.1323237400502 "#9B0064FF" "healthy cortex cell 260" "GSM1658130" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486101" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996120" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658130/GSM1658130_nochipID8.C06.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996120" "GSM1658130_nochipID8.C06.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 22.7349768653512 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 495801 17528 621239 22.7349768653512 "#0000FFFF" "healthy cortex cell 261" "GSM1658131" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486102" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996121" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658131/GSM1658131_nochipID8.C08.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996121" "GSM1658131_nochipID8.C08.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.6697975769639 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1503627 8477 1032342 21.6697975769639 "#4800B7FF" "healthy cortex cell 262" "GSM1658132" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486103" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996122" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658132/GSM1658132_nochipID8.C11.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996122" "GSM1658132_nochipID8.C11.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "hybrid" 21 21 19.7750341873616 "AB_S7" 2 2 "deeppink" 9 3 2 "#8B1A1AFF" "#FFFF00FF" 2075452 10467 1029291 19.7750341873616 "#0000FFFF" "healthy cortex cell 263" "GSM1658133" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486104" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996123" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658133/GSM1658133_nochipID8.C12.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996123" "GSM1658133_nochipID8.C12.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 21.8367450870574 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 1269959 18847 782863 21.8367450870574 "#0000FFFF" "healthy cortex cell 264" "GSM1658134" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486105" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996124" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658134/GSM1658134_nochipID8.C13.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996124" "GSM1658134_nochipID8.C13.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.9909036159515 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1274559 6937 746268 20.9909036159515 "#73008CFF" "healthy cortex cell 265" "GSM1658135" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486106" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996125" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658135/GSM1658135_nochipID8.C14.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996125" "GSM1658135_nochipID8.C14.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.2155108610168 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1149201 5758 941358 20.2155108610168 "#3E00C1FF" "healthy cortex cell 266" "GSM1658136" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486107" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996126" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658136/GSM1658136_nochipID8.C17.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996126" "GSM1658136_nochipID8.C17.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 19.0646726423874 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1293386 11704 1240772 19.0646726423874 "#0000FFFF" "healthy cortex cell 267" "GSM1658137" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486108" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996127" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658137/GSM1658137_nochipID8.C19.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996127" "GSM1658137_nochipID8.C19.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.415106809698 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 841301 11160 791255 20.415106809698 "#7B0084FF" "healthy cortex cell 268" "GSM1658138" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486109" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996128" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658138/GSM1658138_nochipID8.C20.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996128" "GSM1658138_nochipID8.C20.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.8942387336865 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 521861 5925 473693 20.8942387336865 "#0000FFFF" "healthy cortex cell 269" "GSM1658139" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486110" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996129" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658139/GSM1658139_nochipID8.C22.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996129" "GSM1658139_nochipID8.C22.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 22.6784898424521 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 525407 3172 387590 22.6784898424521 "#65009AFF" "healthy cortex cell 270" "GSM1658140" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486111" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996130" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658140/GSM1658140_nochipID8.C23.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996130" "GSM1658140_nochipID8.C23.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 20.6040418399498 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 1295163 14340 856014 20.6040418399498 "#0000FFFF" "healthy cortex cell 271" "GSM1658141" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486112" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996131" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658141/GSM1658141_nochipID8.C25.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996131" "GSM1658141_nochipID8.C25.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 19.9224240425974 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 754874 14362 823984 19.9224240425974 "#860079FF" "healthy cortex cell 272" "GSM1658142" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486113" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996132" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658142/GSM1658142_nochipID8.C28.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996132" "GSM1658142_nochipID8.C28.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "astrocytes" 21 21 22.558430660516 "AB_S7" 2 2 "yellow" 22 3 2 "#8B1A1AFF" "#FFFF00FF" 666621 4875 361936 22.558430660516 "#0000FFFF" "healthy cortex cell 273" "GSM1658143" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486114" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996133" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658143/GSM1658143_nochipID8.C29.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996133" "GSM1658143_nochipID8.C29.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.8296504933387 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1359159 7299 648884 20.8296504933387 "#890076FF" "healthy cortex cell 274" "GSM1658144" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486115" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996134" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658144/GSM1658144_nochipID8.C30.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996134" "GSM1658144_nochipID8.C30.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "hybrid" 21 21 22.987452047877 "AB_S7" 2 2 "deeppink" 9 3 2 "#8B1A1AFF" "#FFFF00FF" 200621 3296 196958 22.987452047877 "#64009BFF" "healthy cortex cell 275" "GSM1658145" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486056" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996135" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658145/GSM1658145_nochipID8.C32.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996135" "GSM1658145_nochipID8.C32.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.4540309980512 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 999707 5611 542651 20.4540309980512 "#8C0073FF" "healthy cortex cell 276" "GSM1658146" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486057" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996136" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658146/GSM1658146_nochipID8.C36.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996136" "GSM1658146_nochipID8.C36.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.7310510193929 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 865485 4320 415868 21.7310510193929 "#A4005BFF" "healthy cortex cell 277" "GSM1658147" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486058" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996137" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658147/GSM1658147_nochipID8.C37.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996137" "GSM1658147_nochipID8.C37.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 19.5429065646604 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 802933 10771 665909 19.5429065646604 "#A4005BFF" "healthy cortex cell 278" "GSM1658148" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486059" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996138" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658148/GSM1658148_nochipID8.C39.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996138" "GSM1658148_nochipID8.C39.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 22.4092623982579 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1018081 9706 739676 22.4092623982579 "#4600B9FF" "healthy cortex cell 279" "GSM1658149" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486060" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996139" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658149/GSM1658149_nochipID8.C40.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996139" "GSM1658149_nochipID8.C40.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.2713384320959 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1444632 4379 839594 20.2713384320959 "#8B0074FF" "healthy cortex cell 280" "GSM1658150" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486061" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996140" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658150/GSM1658150_nochipID8.C41.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996140" "GSM1658150_nochipID8.C41.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 22.0930893830955 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1761294 8636 950097 22.0930893830955 "#5200ADFF" "healthy cortex cell 281" "GSM1658151" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486062" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996141" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658151/GSM1658151_nochipID8.C42.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996141" "GSM1658151_nochipID8.C42.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 22.0431252354756 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 498297 2819 232048 22.0431252354756 "#2D00D2FF" "healthy cortex cell 282" "GSM1658152" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486063" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996142" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658152/GSM1658152_nochipID8.C43.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996142" "GSM1658152_nochipID8.C43.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 19.7645284943283 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1388688 4995 815534 19.7645284943283 "#4C00B3FF" "healthy cortex cell 283" "GSM1658153" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486064" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996143" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658153/GSM1658153_nochipID8.C45.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996143" "GSM1658153_nochipID8.C45.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.7891100319102 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1170904 10058 876001 21.7891100319102 "#0000FFFF" "healthy cortex cell 284" "GSM1658154" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486065" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996144" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658154/GSM1658154_nochipID8.C48.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996144" "GSM1658154_nochipID8.C48.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "hybrid" 21 21 19.5274755451828 "AB_S7" 2 2 "deeppink" 9 3 2 "#8B1A1AFF" "#FFFF00FF" 1250030 8073 562364 19.5274755451828 "#1400EBFF" "healthy cortex cell 285" "GSM1658155" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486066" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996145" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658155/GSM1658155_nochipID8.C49.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996145" "GSM1658155_nochipID8.C49.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 21.8344524484128 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 663962 14980 677895 21.8344524484128 "#0000FFFF" "healthy cortex cell 286" "GSM1658156" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486067" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996146" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658156/GSM1658156_nochipID8.C50.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996146" "GSM1658156_nochipID8.C50.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.1327492082492 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1450507 12849 925309 20.1327492082492 "#BF0040FF" "healthy cortex cell 287" "GSM1658157" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486068" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996147" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658157/GSM1658157_nochipID8.C52.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996147" "GSM1658157_nochipID8.C52.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 22.2881231894717 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 729358 12358 572030 22.2881231894717 "#5C00A3FF" "healthy cortex cell 288" "GSM1658158" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486069" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996148" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658158/GSM1658158_nochipID8.C53.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996148" "GSM1658158_nochipID8.C53.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.9396891836077 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1259910 9711 638270 20.9396891836077 "#5500AAFF" "healthy cortex cell 289" "GSM1658159" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486070" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996149" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658159/GSM1658159_nochipID8.C54.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996149" "GSM1658159_nochipID8.C54.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 21.3036551307887 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 625538 22471 624812 21.3036551307887 "#0000FFFF" "healthy cortex cell 290" "GSM1658160" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486071" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996150" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658160/GSM1658160_nochipID8.C55.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996150" "GSM1658160_nochipID8.C55.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.1490845568478 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1253342 10798 774700 21.1490845568478 "#A0005FFF" "healthy cortex cell 291" "GSM1658161" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486072" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996151" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658161/GSM1658161_nochipID8.C56.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996151" "GSM1658161_nochipID8.C56.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "hybrid" 21 21 20.9182439632714 "AB_S7" 2 2 "deeppink" 9 3 2 "#8B1A1AFF" "#FFFF00FF" 1071691 8661 715938 20.9182439632714 "#0000FFFF" "healthy cortex cell 292" "GSM1658162" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486073" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996152" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658162/GSM1658162_nochipID8.C57.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996152" "GSM1658162_nochipID8.C57.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 21.1427449444309 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 1139652 18798 761322 21.1427449444309 "#1400EBFF" "healthy cortex cell 293" "GSM1658163" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486074" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996153" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658163/GSM1658163_nochipID8.C60.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996153" "GSM1658163_nochipID8.C60.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 19.4469071794301 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 625908 8550 399128 19.4469071794301 "#72008DFF" "healthy cortex cell 294" "GSM1658164" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486075" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996154" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658164/GSM1658164_nochipID8.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996154" "GSM1658164_nochipID8.C61.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 21.2297234619036 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 1098031 15174 637260 21.2297234619036 "#0000FFFF" "healthy cortex cell 295" "GSM1658165" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486076" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996155" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658165/GSM1658165_nochipID8.C64.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996155" "GSM1658165_nochipID8.C64.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "hybrid" 21 21 22.3694251030684 "AB_S7" 2 2 "deeppink" 9 3 2 "#8B1A1AFF" "#FFFF00FF" 1899465 11184 814713 22.3694251030684 "#880077FF" "healthy cortex cell 296" "GSM1658166" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486077" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996156" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658166/GSM1658166_nochipID8.C65.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996156" "GSM1658166_nochipID8.C65.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.3603143999353 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1284924 10775 626783 21.3603143999353 "#0000FFFF" "healthy cortex cell 297" "GSM1658167" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486078" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996157" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658167/GSM1658167_nochipID8.C66.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996157" "GSM1658167_nochipID8.C66.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 19.3880223417655 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 1618098 15418 683987 19.3880223417655 "#0000FFFF" "healthy cortex cell 298" "GSM1658168" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486085" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996158" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658168/GSM1658168_nochipID8.C67.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996158" "GSM1658168_nochipID8.C67.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "astrocytes" 21 21 22.0565875126049 "AB_S7" 2 2 "yellow" 22 3 2 "#8B1A1AFF" "#FFFF00FF" 1468866 8973 775498 22.0565875126049 "#0000FFFF" "healthy cortex cell 299" "GSM1658169" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486026" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996159" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658169/GSM1658169_nochipID8.C70.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996159" "GSM1658169_nochipID8.C70.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.3071371698752 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1558864 9461 801743 21.3071371698752 "#1400EBFF" "healthy cortex cell 300" "GSM1658170" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486027" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996160" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658170/GSM1658170_nochipID8.C75.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996160" "GSM1658170_nochipID8.C75.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.8089312566444 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1233853 10160 677372 21.8089312566444 "#9B0064FF" "healthy cortex cell 301" "GSM1658171" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486079" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996161" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658171/GSM1658171_nochipID8.C77.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996161" "GSM1658171_nochipID8.C77.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.0515899872407 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1275477 10554 889173 20.0515899872407 "#A60059FF" "healthy cortex cell 302" "GSM1658172" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486080" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996162" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658172/GSM1658172_nochipID8.C78.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996162" "GSM1658172_nochipID8.C78.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.7368754567578 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 949377 10309 781470 20.7368754567578 "#80007FFF" "healthy cortex cell 303" "GSM1658173" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486081" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996163" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658173/GSM1658173_nochipID8.C79.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996163" "GSM1658173_nochipID8.C79.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 22.8571617603302 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 1343260 15122 672250 22.8571617603302 "#0000FFFF" "healthy cortex cell 304" "GSM1658174" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486082" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996164" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658174/GSM1658174_nochipID8.C81.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996164" "GSM1658174_nochipID8.C81.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "astrocytes" 21 21 22.8644931968302 "AB_S7" 2 2 "yellow" 22 3 2 "#8B1A1AFF" "#FFFF00FF" 1908841 8477 735408 22.8644931968302 "#0000FFFF" "healthy cortex cell 305" "GSM1658175" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486083" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996165" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658175/GSM1658175_nochipID8.C82.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996165" "GSM1658175_nochipID8.C82.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.0420291423798 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1784285 8213 1080074 21.0420291423798 "#0000FFFF" "healthy cortex cell 306" "GSM1658176" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486084" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996166" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658176/GSM1658176_nochipID8.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996166" "GSM1658176_nochipID8.C84.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 22.3578870352358 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1097120 8882 708826 22.3578870352358 "#890076FF" "healthy cortex cell 307" "GSM1658177" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486028" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996167" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658177/GSM1658177_nochipID8.C85.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996167" "GSM1658177_nochipID8.C85.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 19.5902052335441 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 1653825 13529 902293 19.5902052335441 "#1400EBFF" "healthy cortex cell 308" "GSM1658178" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486029" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996168" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658178/GSM1658178_nochipID8.C87.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996168" "GSM1658178_nochipID8.C87.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "hybrid" 21 21 20.5904776826501 "AB_S7" 2 2 "deeppink" 9 3 2 "#8B1A1AFF" "#FFFF00FF" 1903540 9388 868256 20.5904776826501 "#C0003FFF" "healthy cortex cell 309" "GSM1658179" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486030" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996169" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658179/GSM1658179_nochipID8.C88.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996169" "GSM1658179_nochipID8.C88.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 21.8768407069147 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 2048857 13917 1126149 21.8768407069147 "#9C0063FF" "healthy cortex cell 310" "GSM1658180" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: oligodendrocytes" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486031" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996170" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658180/GSM1658180_nochipID8.C90.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996170" "GSM1658180_nochipID8.C90.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "oligodendrocytes" 21 21 19.6890665199608 "AB_S7" 2 2 "dodgerblue" 24 3 2 "#8B1A1AFF" "#FFFF00FF" 1641063 15221 995837 19.6890665199608 "#0000FFFF" "healthy cortex cell 311" "GSM1658181" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486032" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996171" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658181/GSM1658181_nochipID8.C92.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996171" "GSM1658181_nochipID8.C92.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 20.7903261389583 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 856704 4106 391916 20.7903261389583 "#3300CCFF" "healthy cortex cell 312" "GSM1658182" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486033" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996172" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658182/GSM1658182_nochipID8.C95.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996172" "GSM1658182_nochipID8.C95.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "neurons" 21 21 21.7684636479244 "AB_S7" 2 2 "red" 21 3 2 "#8B1A1AFF" "#FFFF00FF" 2040032 14902 972128 21.7684636479244 "#B5004AFF" "healthy cortex cell 313" "GSM1658183" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: hybrid" "age: postnatal 21 years" "c1 chip id: nochipID8" "experiment_sample_name: AB_S7" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486034" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996173" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658183/GSM1658183_nochipID8.C96.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996173" "GSM1658183_nochipID8.C96.csv" "Illumina NextSeq 500" "nochipID8" "TemporalLobe" "hybrid" 21 21 22.8935599783435 "AB_S7" 2 2 "deeppink" 9 3 2 "#8B1A1AFF" "#FFFF00FF" 1237623 13603 796019 22.8935599783435 "#7A0085FF" "healthy cortex cell 314" "GSM1658184" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486035" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996174" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658184/GSM1658184_nochipID9.C01.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996174" "GSM1658184_nochipID9.C01.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 44.9797807568684 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 752610 6899 480123 44.9797807568684 "#0000FFFF" "healthy cortex cell 315" "GSM1658185" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486036" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996175" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658185/GSM1658185_nochipID9.C02.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996175" "GSM1658185_nochipID9.C02.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 44.0693596955389 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 450473 1256 214111 44.0693596955389 "#0000FFFF" "healthy cortex cell 316" "GSM1658186" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486037" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996176" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658186/GSM1658186_nochipID9.C04.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996176" "GSM1658186_nochipID9.C04.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 44.0105658117682 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 820765 762 440392 44.0105658117682 "#0000FFFF" "healthy cortex cell 317" "GSM1658187" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486038" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996177" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658187/GSM1658187_nochipID9.C09.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996177" "GSM1658187_nochipID9.C09.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 44.7724157087505 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 289481 3759 197852 44.7724157087505 "#0000FFFF" "healthy cortex cell 318" "GSM1658188" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486039" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996178" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658188/GSM1658188_nochipID9.C14.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996178" "GSM1658188_nochipID9.C14.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "microglia" 47 47 47.12188783288 "AB_S1" 5 2 "springgreen" 7 7 1 "#000000FF" "#8A2BE2FF" 291694 1500 393096 47.12188783288 "#1400EBFF" "healthy cortex cell 319" "GSM1658189" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486040" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996179" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658189/GSM1658189_nochipID9.C18.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996179" "GSM1658189_nochipID9.C18.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "microglia" 47 47 46.9414145890623 "AB_S1" 5 2 "springgreen" 7 7 1 "#000000FF" "#8A2BE2FF" 268141 5981 413143 46.9414145890623 "#1400EBFF" "healthy cortex cell 320" "GSM1658190" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486041" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996180" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658190/GSM1658190_nochipID9.C26.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996180" "GSM1658190_nochipID9.C26.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 44.3562637576833 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 601505 3838 346240 44.3562637576833 "#1400EBFF" "healthy cortex cell 321" "GSM1658191" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486042" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996181" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658191/GSM1658191_nochipID9.C37.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996181" "GSM1658191_nochipID9.C37.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 45.2833135649562 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 605403 814 275630 45.2833135649562 "#0000FFFF" "healthy cortex cell 322" "GSM1658192" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486043" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996182" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658192/GSM1658192_nochipID9.C42.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996182" "GSM1658192_nochipID9.C42.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "neurons" 47 47 44.5412935437635 "AB_S1" 5 2 "red" 21 7 1 "#000000FF" "#8A2BE2FF" 863317 6349 458308 44.5412935437635 "#960069FF" "healthy cortex cell 323" "GSM1658193" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486045" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996183" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658193/GSM1658193_nochipID9.C57.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996183" "GSM1658193_nochipID9.C57.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 47.4662204273045 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 756041 4743 362158 47.4662204273045 "#0000FFFF" "healthy cortex cell 324" "GSM1658194" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486046" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996184" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658194/GSM1658194_nochipID9.C59.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996184" "GSM1658194_nochipID9.C59.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "neurons" 47 47 46.4553071632981 "AB_S1" 5 2 "red" 21 7 1 "#000000FF" "#8A2BE2FF" 1273305 1070 494347 46.4553071632981 "#0000FFFF" "healthy cortex cell 325" "GSM1658195" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486047" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996185" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658195/GSM1658195_nochipID9.C62.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996185" "GSM1658195_nochipID9.C62.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "neurons" 47 47 47.0761432768777 "AB_S1" 5 2 "red" 21 7 1 "#000000FF" "#8A2BE2FF" 1009477 3954 401769 47.0761432768777 "#83007CFF" "healthy cortex cell 326" "GSM1658196" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: microglia" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486048" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996186" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658196/GSM1658196_nochipID9.C65.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996186" "GSM1658196_nochipID9.C65.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "microglia" 47 47 47.7331257676706 "AB_S1" 5 2 "springgreen" 7 7 1 "#000000FF" "#8A2BE2FF" 1286197 7233 768013 47.7331257676706 "#0000FFFF" "healthy cortex cell 327" "GSM1658197" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486049" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996187" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658197/GSM1658197_nochipID9.C74.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996187" "GSM1658197_nochipID9.C74.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "neurons" 47 47 46.482065377757 "AB_S1" 5 2 "red" 21 7 1 "#000000FF" "#8A2BE2FF" 479090 583 251235 46.482065377757 "#1400EBFF" "healthy cortex cell 328" "GSM1658198" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486050" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996188" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658198/GSM1658198_nochipID9.C75.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996188" "GSM1658198_nochipID9.C75.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "neurons" 47 47 44.1589191686362 "AB_S1" 5 2 "red" 21 7 1 "#000000FF" "#8A2BE2FF" 371356 1710 240023 44.1589191686362 "#0000FFFF" "healthy cortex cell 329" "GSM1658199" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486051" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996189" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658199/GSM1658199_nochipID9.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996189" "GSM1658199_nochipID9.C84.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 46.858386204578 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 1146691 2607 448771 46.858386204578 "#3300CCFF" "healthy cortex cell 330" "GSM1658200" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: neurons" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486052" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996190" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658200/GSM1658200_nochipID9.C85.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996190" "GSM1658200_nochipID9.C85.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "neurons" 47 47 46.660776745528 "AB_S1" 5 2 "red" 21 7 1 "#000000FF" "#8A2BE2FF" 385772 4596 289414 46.660776745528 "#1400EBFF" "healthy cortex cell 331" "GSM1658201" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486044" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996191" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658201/GSM1658201_nochipID9.C87.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996191" "GSM1658201_nochipID9.C87.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 47.8442769963294 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 737563 7376 338755 47.8442769963294 "#1F00E0FF" "healthy cortex cell 332" "GSM1658202" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: astrocytes" "age: postnatal 47 years" "c1 chip id: nochipID9" "experiment_sample_name: AB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486053" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996192" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658202/GSM1658202_nochipID9.C92.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996192" "GSM1658202_nochipID9.C92.csv" "Illumina MiSeq" "nochipID9" "TemporalLobe" "astrocytes" 47 47 45.09300092794 "AB_S1" 5 2 "yellow" 22 7 1 "#000000FF" "#8A2BE2FF" 806708 2587 315073 45.09300092794 "#0000FFFF" "healthy cortex cell 333" "GSM1658203" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486054" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996193" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658203/GSM1658203_nochipID10.C02.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996193" "GSM1658203_nochipID10.C02.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -0.880647792071104 -24.8806477920711 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1241682 7414 547226 -24.8806477920711 "#7B0084FF" "healthy cortex cell 334" "GSM1658204" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486055" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996194" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658204/GSM1658204_nochipID10.C03.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996194" "GSM1658204_nochipID10.C03.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -0.426340435221791 -24.4263404352218 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 496648 11610 362471 -24.4263404352218 "#4600B9FF" "healthy cortex cell 335" "GSM1658205" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485996" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996195" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658205/GSM1658205_nochipID10.C05.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996195" "GSM1658205_nochipID10.C05.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 0.595917309112847 -23.4040826908872 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1175267 4741 318102 -23.4040826908872 "#E1001EFF" "healthy cortex cell 336" "GSM1658206" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485997" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996196" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658206/GSM1658206_nochipID10.C07.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996196" "GSM1658206_nochipID10.C07.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -1.12358683865517 -25.1235868386552 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 865960 7431 421513 -25.1235868386552 "#980067FF" "healthy cortex cell 337" "GSM1658207" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485998" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996197" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658207/GSM1658207_nochipID10.C11.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996197" "GSM1658207_nochipID10.C11.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 0.378364946171641 -23.6216350538284 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1295718 8135 446287 -23.6216350538284 "#2D00D2FF" "healthy cortex cell 338" "GSM1658208" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485999" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996198" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658208/GSM1658208_nochipID10.C16.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996198" "GSM1658208_nochipID10.C16.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 1.49724829424173 -22.5027517057583 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1354202 5424 427428 -22.5027517057583 "#2D00D2FF" "healthy cortex cell 339" "GSM1658209" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486000" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996199" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658209/GSM1658209_nochipID10.C17.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996199" "GSM1658209_nochipID10.C17.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -0.537863296046853 -24.5378632960469 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 938472 3843 389069 -24.5378632960469 "#AE0051FF" "healthy cortex cell 340" "GSM1658210" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486001" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996200" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658210/GSM1658210_nochipID10.C19.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996200" "GSM1658210_nochipID10.C19.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -1.10330382507294 -25.1033038250729 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 927649 6839 395054 -25.1033038250729 "#2700D8FF" "healthy cortex cell 341" "GSM1658211" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486002" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996201" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658211/GSM1658211_nochipID10.C25.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996201" "GSM1658211_nochipID10.C25.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -0.120883566848934 -24.1208835668489 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1141672 12361 524531 -24.1208835668489 "#D70028FF" "healthy cortex cell 342" "GSM1658212" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486003" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996202" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658212/GSM1658212_nochipID10.C26.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996202" "GSM1658212_nochipID10.C26.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -0.310682476088405 -24.3106824760884 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 830265 13867 362433 -24.3106824760884 "#E80017FF" "healthy cortex cell 343" "GSM1658213" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486004" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996203" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658213/GSM1658213_nochipID10.C37.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996203" "GSM1658213_nochipID10.C37.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 1.19591650035232 -22.8040834996477 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1160757 8143 542787 -22.8040834996477 "#81007EFF" "healthy cortex cell 344" "GSM1658214" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486005" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996204" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658214/GSM1658214_nochipID10.C39.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996204" "GSM1658214_nochipID10.C39.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 1.10911234602332 -22.8908876539767 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1015272 8196 435677 -22.8908876539767 "#B5004AFF" "healthy cortex cell 345" "GSM1658215" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486006" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996205" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658215/GSM1658215_nochipID10.C42.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996205" "GSM1658215_nochipID10.C42.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -0.585061797462404 -24.5850617974624 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 808799 11558 720975 -24.5850617974624 "#3300CCFF" "healthy cortex cell 346" "GSM1658216" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486007" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996206" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658216/GSM1658216_nochipID10.C44.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996206" "GSM1658216_nochipID10.C44.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -0.127482237815857 -24.1274822378159 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1174678 5478 574283 -24.1274822378159 "#AA0055FF" "healthy cortex cell 347" "GSM1658217" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486008" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996207" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658217/GSM1658217_nochipID10.C47.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996207" "GSM1658217_nochipID10.C47.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -1.17999982420355 -25.1799998242036 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 844002 5032 404172 -25.1799998242036 "#4400BBFF" "healthy cortex cell 348" "GSM1658218" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486009" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996208" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658218/GSM1658218_nochipID10.C49.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996208" "GSM1658218_nochipID10.C49.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -1.74070930253714 -25.7407093025371 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1089658 8610 500696 -25.7407093025371 "#4C00B3FF" "healthy cortex cell 349" "GSM1658219" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486010" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996209" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658219/GSM1658219_nochipID10.C50.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996209" "GSM1658219_nochipID10.C50.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -0.782095758765936 -24.7820957587659 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1274879 10421 528973 -24.7820957587659 "#4B00B4FF" "healthy cortex cell 350" "GSM1658220" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486011" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996210" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658220/GSM1658220_nochipID10.C53.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996210" "GSM1658220_nochipID10.C53.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 0.508460812680423 -23.4915391873196 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 761705 5400 352092 -23.4915391873196 "#A70058FF" "healthy cortex cell 351" "GSM1658221" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486012" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996211" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658221/GSM1658221_nochipID10.C58.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996211" "GSM1658221_nochipID10.C58.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalQui" -0.44 1.33858410030603 -22.661415899694 "FB_S1" 1 1 "orange" 4 21 1 "#0000FFFF" "#FFA500FF" 1441995 6743 577274 -22.661415899694 "#8B0074FF" "healthy cortex cell 352" "GSM1658222" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486013" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996212" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658222/GSM1658222_nochipID10.C65.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996212" "GSM1658222_nochipID10.C65.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -1.99365830846131 -25.9936583084613 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 864850 4906 357916 -25.9936583084613 "#C0003FFF" "healthy cortex cell 353" "GSM1658223" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486014" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996213" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658223/GSM1658223_nochipID10.C74.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996213" "GSM1658223_nochipID10.C74.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalQui" -0.44 1.10962961375713 -22.8903703862429 "FB_S1" 1 1 "orange" 4 21 1 "#0000FFFF" "#FFA500FF" 868485 10398 428515 -22.8903703862429 "#A80057FF" "healthy cortex cell 354" "GSM1658224" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486015" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996214" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658224/GSM1658224_nochipID10.C75.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996214" "GSM1658224_nochipID10.C75.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 1.41193688515574 -22.5880631148443 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 612073 9597 339986 -22.5880631148443 "#0000FFFF" "healthy cortex cell 355" "GSM1658225" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486016" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996215" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658225/GSM1658225_nochipID10.C85.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996215" "GSM1658225_nochipID10.C85.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalQui" -0.44 -1.99458521191031 -25.9945852119103 "FB_S1" 1 1 "orange" 4 21 1 "#0000FFFF" "#FFA500FF" 1516605 4263 534291 -25.9945852119103 "#EF0010FF" "healthy cortex cell 356" "GSM1658226" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486017" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996216" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658226/GSM1658226_nochipID10.C88.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996216" "GSM1658226_nochipID10.C88.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalQui" -0.44 0.564268155433238 -23.4357318445668 "FB_S1" 1 1 "orange" 4 21 1 "#0000FFFF" "#FFA500FF" 1104084 7327 505941 -23.4357318445668 "#AF0050FF" "healthy cortex cell 357" "GSM1658227" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486018" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996217" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658227/GSM1658227_nochipID10.C93.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996217" "GSM1658227_nochipID10.C93.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalQui" -0.44 -2.22791901469231 -26.2279190146923 "FB_S1" 1 1 "orange" 4 21 1 "#0000FFFF" "#FFA500FF" 571090 10341 503102 -26.2279190146923 "#FE0001FF" "healthy cortex cell 358" "GSM1658228" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID10" "experiment_sample_name: FB_S1" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486019" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996218" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658228/GSM1658228_nochipID10.C94.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996218" "GSM1658228_nochipID10.C94.csv" "Illumina MiSeq" "nochipID10" "Cortex" "fetalRep" -0.44 -1.7869048012048 -25.7869048012048 "FB_S1" 1 1 "orange4" 3 21 1 "#0000FFFF" "#FFA500FF" 1216681 5910 503329 -25.7869048012048 "#E70018FF" "healthy cortex cell 359" "GSM1658229" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485967" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996219" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658229/GSM1658229_nochipID11.C02.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996219" "GSM1658229_nochipID11.C02.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.45410285849124 -9.45410285849124 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 662866 8534 453106 -9.45410285849124 "#E3001CFF" "healthy cortex cell 360" "GSM1658230" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485968" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996220" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658230/GSM1658230_nochipID11.C03.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996220" "GSM1658230_nochipID11.C03.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -2.04030820500106 -10.0403082050011 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 830679 5263 353707 -10.0403082050011 "#E5001AFF" "healthy cortex cell 361" "GSM1658231" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486020" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996221" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658231/GSM1658231_nochipID11.C06.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996221" "GSM1658231_nochipID11.C06.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.440547363422811 -8.44054736342281 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 619236 10754 537765 -8.44054736342281 "#F90006FF" "healthy cortex cell 362" "GSM1658232" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486021" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996222" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658232/GSM1658232_nochipID11.C07.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996222" "GSM1658232_nochipID11.C07.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.250156400203705 -7.7498435997963 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 303552 4973 202269 -7.7498435997963 "#BD0042FF" "healthy cortex cell 363" "GSM1658233" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486022" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996223" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658233/GSM1658233_nochipID11.C08.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996223" "GSM1658233_nochipID11.C08.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -2.37030519597232 -10.3703051959723 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 889145 6331 384783 -10.3703051959723 "#D0002FFF" "healthy cortex cell 364" "GSM1658234" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486023" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996224" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658234/GSM1658234_nochipID11.C10.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996224" "GSM1658234_nochipID11.C10.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.791576608493924 -7.20842339150608 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 917750 7241 403061 -7.20842339150608 "#DD0022FF" "healthy cortex cell 365" "GSM1658235" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486024" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996225" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658235/GSM1658235_nochipID11.C15.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996225" "GSM1658235_nochipID11.C15.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.46827693335712 -8.46827693335712 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 613154 7424 532929 -8.46827693335712 "#EE0011FF" "healthy cortex cell 366" "GSM1658236" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03486025" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996226" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658236/GSM1658236_nochipID11.C17.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996226" "GSM1658236_nochipID11.C17.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -2.03468394797295 -10.034683947973 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 703769 5835 326740 -10.034683947973 "#DC0023FF" "healthy cortex cell 367" "GSM1658237" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485966" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996227" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658237/GSM1658237_nochipID11.C19.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996227" "GSM1658237_nochipID11.C19.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.06409550976008 -9.06409550976008 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 727980 9579 511799 -9.06409550976008 "#E90016FF" "healthy cortex cell 368" "GSM1658238" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485969" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996228" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658238/GSM1658238_nochipID11.C20.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996228" "GSM1658238_nochipID11.C20.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -2.29407283902168 -10.2940728390217 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 651652 7629 298138 -10.2940728390217 "#D4002BFF" "healthy cortex cell 369" "GSM1658239" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485970" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996229" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658239/GSM1658239_nochipID11.C21.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996229" "GSM1658239_nochipID11.C21.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.445478229261935 -7.55452177073807 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1124407 4264 387281 -7.55452177073807 "#E2001DFF" "healthy cortex cell 370" "GSM1658240" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485971" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996230" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658240/GSM1658240_nochipID11.C22.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996230" "GSM1658240_nochipID11.C22.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.767318807020783 -7.23268119297922 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 598621 4797 427016 -7.23268119297922 "#E3001CFF" "healthy cortex cell 371" "GSM1658241" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485972" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996231" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658241/GSM1658241_nochipID11.C23.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996231" "GSM1658241_nochipID11.C23.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.16995938546956 -9.16995938546956 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1302157 7734 495397 -9.16995938546956 "#D70028FF" "healthy cortex cell 372" "GSM1658242" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485973" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996232" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658242/GSM1658242_nochipID11.C25.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996232" "GSM1658242_nochipID11.C25.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalRep" -0.44 1.48067612614483 -6.51932387385517 "FB_S2" 1 1 "orange4" 3 21 1 "#00FF00FF" "#FF0000FF" 528951 3777 322428 -6.51932387385517 "#1400EBFF" "healthy cortex cell 373" "GSM1658243" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485974" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996233" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658243/GSM1658243_nochipID11.C30.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996233" "GSM1658243_nochipID11.C30.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 1.29575607035309 -6.70424392964691 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 430582 7799 297054 -6.70424392964691 "#ED0012FF" "healthy cortex cell 374" "GSM1658244" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485975" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996234" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658244/GSM1658244_nochipID11.C37.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996234" "GSM1658244_nochipID11.C37.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -2.28405672550201 -10.284056725502 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1118433 8534 508613 -10.284056725502 "#EB0014FF" "healthy cortex cell 375" "GSM1658245" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485976" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996235" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658245/GSM1658245_nochipID11.C48.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996235" "GSM1658245_nochipID11.C48.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.91336649697274 -7.08663350302726 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 807483 5062 238774 -7.08663350302726 "#CD0032FF" "healthy cortex cell 376" "GSM1658246" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485977" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996236" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658246/GSM1658246_nochipID11.C49.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996236" "GSM1658246_nochipID11.C49.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.71474504522979 -9.71474504522979 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 955606 6951 510685 -9.71474504522979 "#DC0023FF" "healthy cortex cell 377" "GSM1658247" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485978" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996237" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658247/GSM1658247_nochipID11.C50.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996237" "GSM1658247_nochipID11.C50.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -2.41868187073618 -10.4186818707362 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 785000 6424 398356 -10.4186818707362 "#E60019FF" "healthy cortex cell 378" "GSM1658248" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485979" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996238" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658248/GSM1658248_nochipID11.C53.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996238" "GSM1658248_nochipID11.C53.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.423206822425127 -7.57679317757487 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 829648 11666 385275 -7.57679317757487 "#DD0022FF" "healthy cortex cell 379" "GSM1658249" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485980" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996239" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658249/GSM1658249_nochipID11.C54.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996239" "GSM1658249_nochipID11.C54.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.0932313916832209 -8.09323139168322 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1333521 8885 506407 -8.09323139168322 "#C70038FF" "healthy cortex cell 380" "GSM1658251" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485981" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996240" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658251/GSM1658251_nochipID11.C55.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996240" "GSM1658251_nochipID11.C55.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 1.09486634138972 -6.90513365861028 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 804967 3929 366152 -6.90513365861028 "#E3001CFF" "healthy cortex cell 381" "GSM1658253" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485982" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996241" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658253/GSM1658253_nochipID11.C56.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996241" "GSM1658253_nochipID11.C56.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.501803460121155 -8.50180346012115 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1062268 4704 364362 -8.50180346012115 "#9E0061FF" "healthy cortex cell 382" "GSM1658255" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485983" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996242" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658255/GSM1658255_nochipID11.C57.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996242" "GSM1658255_nochipID11.C57.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.587537531331181 -8.58753753133118 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1190632 5810 467068 -8.58753753133118 "#DE0021FF" "healthy cortex cell 383" "GSM1658257" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485984" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996243" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658257/GSM1658257_nochipID11.C58.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996243" "GSM1658257_nochipID11.C58.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.597883532233536 -7.40211646776646 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 697843 6274 402189 -7.40211646776646 "#E70018FF" "healthy cortex cell 384" "GSM1658259" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485985" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996244" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658259/GSM1658259_nochipID11.C59.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996244" "GSM1658259_nochipID11.C59.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.965164219550788 -8.96516421955079 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1168946 7248 526427 -8.96516421955079 "#E0001FFF" "healthy cortex cell 385" "GSM1658262" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485986" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996245" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658262/GSM1658262_nochipID11.C60.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996245" "GSM1658262_nochipID11.C60.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.28563794452697 -8.28563794452697 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1438638 8920 641909 -8.28563794452697 "#F3000CFF" "healthy cortex cell 386" "GSM1658264" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485987" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996246" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658264/GSM1658264_nochipID11.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996246" "GSM1658264_nochipID11.C61.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.441918100640178 -7.55808189935982 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 541019 5419 392493 -7.55808189935982 "#85007AFF" "healthy cortex cell 387" "GSM1658266" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485988" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996247" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658266/GSM1658266_nochipID11.C62.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996247" "GSM1658266_nochipID11.C62.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.0447935178503394 -8.04479351785034 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1355720 9799 484254 -8.04479351785034 "#F4000BFF" "healthy cortex cell 388" "GSM1658268" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485989" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996248" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658268/GSM1658268_nochipID11.C63.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996248" "GSM1658268_nochipID11.C63.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.37519994337112 -9.37519994337112 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1245695 7011 442525 -9.37519994337112 "#D5002AFF" "healthy cortex cell 389" "GSM1658270" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485990" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996249" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658270/GSM1658270_nochipID11.C64.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996249" "GSM1658270_nochipID11.C64.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.104845993742347 -8.10484599374235 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1371907 7063 430268 -8.10484599374235 "#D5002AFF" "healthy cortex cell 390" "GSM1658272" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485991" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996250" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658272/GSM1658272_nochipID11.C66.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996250" "GSM1658272_nochipID11.C66.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.677227624170482 -7.32277237582952 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 682259 7928 334502 -7.32277237582952 "#E1001EFF" "healthy cortex cell 391" "GSM1658275" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485992" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996251" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658275/GSM1658275_nochipID11.C68.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996251" "GSM1658275_nochipID11.C68.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.228537889719009 -8.22853788971901 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 754276 6809 374184 -8.22853788971901 "#DD0022FF" "healthy cortex cell 392" "GSM1658277" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485993" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996252" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658277/GSM1658277_nochipID11.C69.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996252" "GSM1658277_nochipID11.C69.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.720341598205268 -8.72034159820527 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 535362 3125 215239 -8.72034159820527 "#D70028FF" "healthy cortex cell 393" "GSM1658279" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485994" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996253" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658279/GSM1658279_nochipID11.C75.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996253" "GSM1658279_nochipID11.C75.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.90251961030066 -9.90251961030066 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1187408 4847 493919 -9.90251961030066 "#D3002CFF" "healthy cortex cell 394" "GSM1658281" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485995" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996254" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658281/GSM1658281_nochipID11.C76.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996254" "GSM1658281_nochipID11.C76.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.686003116481006 -8.68600311648101 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1007373 5549 362092 -8.68600311648101 "#DC0023FF" "healthy cortex cell 395" "GSM1658284" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485936" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996255" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658284/GSM1658284_nochipID11.C77.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996255" "GSM1658284_nochipID11.C77.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.572591180503368 -8.57259118050337 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1257424 7807 499758 -8.57259118050337 "#F4000BFF" "healthy cortex cell 396" "GSM1658286" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485937" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996256" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658286/GSM1658286_nochipID11.C78.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996256" "GSM1658286_nochipID11.C78.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.91181920986623 -9.91181920986623 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 542648 6168 377324 -9.91181920986623 "#DA0025FF" "healthy cortex cell 397" "GSM1658288" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485938" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996257" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658288/GSM1658288_nochipID11.C79.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996257" "GSM1658288_nochipID11.C79.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.268033598959446 -7.73196640104055 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1017541 3612 330167 -7.73196640104055 "#FA0005FF" "healthy cortex cell 398" "GSM1658290" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485939" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996258" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658290/GSM1658290_nochipID11.C81.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996258" "GSM1658290_nochipID11.C81.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.843350055217743 -8.84335005521774 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1096730 7053 457720 -8.84335005521774 "#DF0020FF" "healthy cortex cell 399" "GSM1658292" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485940" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996259" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658292/GSM1658292_nochipID11.C82.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996259" "GSM1658292_nochipID11.C82.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.411305753104389 -8.41130575310439 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 894390 7824 393690 -8.41130575310439 "#ED0012FF" "healthy cortex cell 400" "GSM1658294" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485941" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996260" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658294/GSM1658294_nochipID11.C83.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996260" "GSM1658294_nochipID11.C83.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.37262714147568 -9.37262714147568 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1438854 6638 496915 -9.37262714147568 "#D90026FF" "healthy cortex cell 401" "GSM1658297" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485942" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996261" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658297/GSM1658297_nochipID11.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996261" "GSM1658297_nochipID11.C84.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -0.875948408208787 -8.87594840820879 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 523143 4820 289202 -8.87594840820879 "#EE0011FF" "healthy cortex cell 402" "GSM1658299" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485943" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996262" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658299/GSM1658299_nochipID11.C86.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996262" "GSM1658299_nochipID11.C86.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 -1.95525487937033 -9.95525487937033 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 997108 8637 507832 -9.95525487937033 "#EE0011FF" "healthy cortex cell 403" "GSM1658301" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485944" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996263" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658301/GSM1658301_nochipID11.C91.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996263" "GSM1658301_nochipID11.C91.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalQui" -0.44 0.818806355297566 -7.18119364470243 "FB_S2" 1 1 "orange" 4 21 1 "#00FF00FF" "#FF0000FF" 1378723 9402 569691 -7.18119364470243 "#D5002AFF" "healthy cortex cell 404" "GSM1658304" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID11" "experiment_sample_name: FB_S2" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485945" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996264" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658304/GSM1658304_nochipID11.C93.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996264" "GSM1658304_nochipID11.C93.csv" "Illumina MiSeq" "nochipID11" "Cortex" "fetalRep" -0.44 -1.46513322979212 -9.46513322979212 "FB_S2" 1 1 "orange4" 3 21 1 "#00FF00FF" "#FF0000FF" 484975 2385 146255 -9.46513322979212 "#D1002EFF" "healthy cortex cell 405" "GSM1658305" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485946" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996265" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658305/GSM1658305_nochipID13.C07.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996265" "GSM1658305_nochipID13.C07.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -1.34077293291688 -17.3407729329169 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 597912 4519 398292 -17.3407729329169 "#FF0000FF" "healthy cortex cell 406" "GSM1658306" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485947" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996266" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658306/GSM1658306_nochipID13.C11.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996266" "GSM1658306_nochipID13.C11.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.995908562503755 -15.0040914374962 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 951621 5487 365236 -15.0040914374962 "#DF0020FF" "healthy cortex cell 407" "GSM1658307" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485948" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996267" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658307/GSM1658307_nochipID13.C12.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996267" "GSM1658307_nochipID13.C12.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -0.045141025967896 -16.0451410259679 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 593665 9460 482626 -16.0451410259679 "#EC0013FF" "healthy cortex cell 408" "GSM1658308" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485949" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996268" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658308/GSM1658308_nochipID13.C14.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996268" "GSM1658308_nochipID13.C14.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 1.34444920293987 -14.6555507970601 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 534538 5937 366283 -14.6555507970601 "#D70028FF" "healthy cortex cell 409" "GSM1658309" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485950" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996269" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658309/GSM1658309_nochipID13.C15.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996269" "GSM1658309_nochipID13.C15.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.549106014370918 -15.4508939856291 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 974144 6380 379485 -15.4508939856291 "#E0001FFF" "healthy cortex cell 410" "GSM1658310" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485951" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996270" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658310/GSM1658310_nochipID13.C17.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996270" "GSM1658310_nochipID13.C17.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -2.17329624161124 -18.1732962416112 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 1124447 6932 609720 -18.1732962416112 "#E2001DFF" "healthy cortex cell 411" "GSM1658311" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485952" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996271" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658311/GSM1658311_nochipID13.C21.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996271" "GSM1658311_nochipID13.C21.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.620401251539588 -15.3795987484604 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 716418 3996 296524 -15.3795987484604 "#C60039FF" "healthy cortex cell 412" "GSM1658312" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485953" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996272" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658312/GSM1658312_nochipID13.C25.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996272" "GSM1658312_nochipID13.C25.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -0.24906280875206 -16.2490628087521 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 996081 4783 423307 -16.2490628087521 "#D60029FF" "healthy cortex cell 413" "GSM1658313" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485954" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996273" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658313/GSM1658313_nochipID13.C28.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996273" "GSM1658313_nochipID13.C28.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -0.756919181495905 -16.7569191814959 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 1031130 7747 381576 -16.7569191814959 "#D4002BFF" "healthy cortex cell 414" "GSM1658314" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485955" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996274" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658314/GSM1658314_nochipID13.C32.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996274" "GSM1658314_nochipID13.C32.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -1.72995557315648 -17.7299555731565 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 1259975 5369 493686 -17.7299555731565 "#EF0010FF" "healthy cortex cell 415" "GSM1658315" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485956" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996275" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658315/GSM1658315_nochipID13.C36.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996275" "GSM1658315_nochipID13.C36.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.0797982359677553 -15.9202017640322 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 842373 6670 323290 -15.9202017640322 "#94006BFF" "healthy cortex cell 416" "GSM1658316" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485957" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996276" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658316/GSM1658316_nochipID13.C45.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996276" "GSM1658316_nochipID13.C45.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 1.47159980464727 -14.5284001953527 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 584713 2269 229693 -14.5284001953527 "#9B0064FF" "healthy cortex cell 417" "GSM1658317" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485958" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996277" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658317/GSM1658317_nochipID13.C46.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996277" "GSM1658317_nochipID13.C46.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.489570926353335 -15.5104290736467 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 570446 7266 392224 -15.5104290736467 "#CF0030FF" "healthy cortex cell 418" "GSM1658318" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485959" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996278" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658318/GSM1658318_nochipID13.C48.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996278" "GSM1658318_nochipID13.C48.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 1.11864463094622 -14.8813553690538 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 594906 3028 241740 -14.8813553690538 "#D0002FFF" "healthy cortex cell 419" "GSM1658319" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485960" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996279" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658319/GSM1658319_nochipID13.C50.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996279" "GSM1658319_nochipID13.C50.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -0.074656579233706 -16.0746565792337 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 1000659 8926 377853 -16.0746565792337 "#C90036FF" "healthy cortex cell 420" "GSM1658320" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485961" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996280" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658320/GSM1658320_nochipID13.C55.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996280" "GSM1658320_nochipID13.C55.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.931322105638683 -15.0686778943613 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 1226485 8570 391149 -15.0686778943613 "#FD0002FF" "healthy cortex cell 421" "GSM1658321" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485962" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996281" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658321/GSM1658321_nochipID13.C57.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996281" "GSM1658321_nochipID13.C57.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -0.145311633646488 -16.1453116336465 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 953955 5325 360068 -16.1453116336465 "#D0002FFF" "healthy cortex cell 422" "GSM1658322" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485963" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996282" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658322/GSM1658322_nochipID13.C58.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996282" "GSM1658322_nochipID13.C58.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 1.50109684322029 -14.4989031567797 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 762412 6898 334387 -14.4989031567797 "#E2001DFF" "healthy cortex cell 423" "GSM1658323" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485964" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996283" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658323/GSM1658323_nochipID13.C59.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996283" "GSM1658323_nochipID13.C59.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 1.49554311338812 -14.5044568866119 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 667000 9906 371666 -14.5044568866119 "#E3001CFF" "healthy cortex cell 424" "GSM1658324" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485965" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996284" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658324/GSM1658324_nochipID13.C61.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996284" "GSM1658324_nochipID13.C61.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -0.472954183407128 -16.4729541834071 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 1293437 6142 422644 -16.4729541834071 "#B4004BFF" "healthy cortex cell 425" "GSM1658325" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485906" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996285" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658325/GSM1658325_nochipID13.C63.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996285" "GSM1658325_nochipID13.C63.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.975402566082776 -15.0245974339172 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 616146 2951 254918 -15.0245974339172 "#CB0034FF" "healthy cortex cell 426" "GSM1658326" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485907" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996286" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658326/GSM1658326_nochipID13.C64.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996286" "GSM1658326_nochipID13.C64.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.469317022189498 -15.5306829778105 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 824580 5415 384722 -15.5306829778105 "#C4003BFF" "healthy cortex cell 427" "GSM1658327" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485908" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996287" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658327/GSM1658327_nochipID13.C66.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996287" "GSM1658327_nochipID13.C66.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -2.38904091209173 -18.3890409120917 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 776021 6044 428607 -18.3890409120917 "#63009CFF" "healthy cortex cell 428" "GSM1658328" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485909" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996288" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658328/GSM1658328_nochipID13.C67.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996288" "GSM1658328_nochipID13.C67.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.464392595402896 -15.5356074045971 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 726410 6933 384950 -15.5356074045971 "#E3001CFF" "healthy cortex cell 429" "GSM1658329" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485910" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996289" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658329/GSM1658329_nochipID13.C68.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996289" "GSM1658329_nochipID13.C68.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.202149349674582 -15.7978506503254 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 783466 4129 268969 -15.7978506503254 "#E3001CFF" "healthy cortex cell 430" "GSM1658330" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485911" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996290" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658330/GSM1658330_nochipID13.C72.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996290" "GSM1658330_nochipID13.C72.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.746227654106915 -15.2537723458931 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 866128 4594 371589 -15.2537723458931 "#CF0030FF" "healthy cortex cell 431" "GSM1658331" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485912" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996291" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658331/GSM1658331_nochipID13.C73.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996291" "GSM1658331_nochipID13.C73.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -1.69763599481434 -17.6976359948143 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 975129 2774 367451 -17.6976359948143 "#EB0014FF" "healthy cortex cell 432" "GSM1658332" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485913" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996292" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658332/GSM1658332_nochipID13.C74.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996292" "GSM1658332_nochipID13.C74.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -2.18420233722776 -18.1842023372278 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 918305 6690 412194 -18.1842023372278 "#DD0022FF" "healthy cortex cell 433" "GSM1658333" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485914" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996293" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658333/GSM1658333_nochipID13.C75.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996293" "GSM1658333_nochipID13.C75.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -0.194216256551445 -16.1942162565514 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 567107 3518 282466 -16.1942162565514 "#BB0044FF" "healthy cortex cell 434" "GSM1658334" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485915" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996294" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658334/GSM1658334_nochipID13.C80.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996294" "GSM1658334_nochipID13.C80.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -1.30918262206018 -17.3091826220602 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 585223 3254 240808 -17.3091826220602 "#C90036FF" "healthy cortex cell 435" "GSM1658335" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485916" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996295" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658335/GSM1658335_nochipID13.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996295" "GSM1658335_nochipID13.C84.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.624703309908509 -15.3752966900915 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 1040925 5909 371327 -15.3752966900915 "#CC0033FF" "healthy cortex cell 436" "GSM1658336" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485917" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996296" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658336/GSM1658336_nochipID13.C87.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996296" "GSM1658336_nochipID13.C87.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 -1.43537538737059 -17.4353753873706 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 583436 9371 356050 -17.4353753873706 "#D60029FF" "healthy cortex cell 437" "GSM1658337" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID13" "experiment_sample_name: FB_S3" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL15520" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina MiSeq" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485918" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996297" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658337/GSM1658337_nochipID13.C93.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996297" "GSM1658337_nochipID13.C93.csv" "Illumina MiSeq" "nochipID13" "TemporalLobe" "fetalQui" -0.44 0.117393065653741 -15.8826069343463 "FB_S3" 1 2 "orange" 4 21 1 "#FFFF00FF" "#FF0000FF" 461467 7832 399641 -15.8826069343463 "#A80057FF" "healthy cortex cell 438" "GSM1658338" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485919" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996298" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658338/GSM1658338_nochipID4.C03.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996298" "GSM1658338_nochipID4.C03.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -1.22492397069931 -1.22492397069931 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 506533 2894 304925 -1.22492397069931 "#BB0044FF" "healthy cortex cell 439" "GSM1658339" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485920" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996299" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658339/GSM1658339_nochipID4.C04.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996299" "GSM1658339_nochipID4.C04.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 1.16198983270675 1.16198983270675 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 1224836 7581 827832 1.16198983270675 "#CF0030FF" "healthy cortex cell 440" "GSM1658340" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485921" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996300" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658340/GSM1658340_nochipID4.C10.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996300" "GSM1658340_nochipID4.C10.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 0.311569530926645 0.311569530926645 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 654178 7564 547446 0.311569530926645 "#D0002FFF" "healthy cortex cell 441" "GSM1658341" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485922" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996301" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658341/GSM1658341_nochipID4.C14.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996301" "GSM1658341_nochipID4.C14.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 0.121950816772878 0.121950816772878 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 754944 4606 504739 0.121950816772878 "#EB0014FF" "healthy cortex cell 442" "GSM1658342" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485923" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996302" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658342/GSM1658342_nochipID4.C18.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996302" "GSM1658342_nochipID4.C18.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 0.727583560571075 0.727583560571075 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 630088 5207 613119 0.727583560571075 "#90006FFF" "healthy cortex cell 443" "GSM1658343" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485924" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996303" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658343/GSM1658343_nochipID4.C19.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996303" "GSM1658343_nochipID4.C19.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -0.9861554704234 -0.9861554704234 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 656340 4517 481424 -0.9861554704234 "#CE0031FF" "healthy cortex cell 444" "GSM1658344" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485925" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996304" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658344/GSM1658344_nochipID4.C20.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996304" "GSM1658344_nochipID4.C20.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -1.49170929711312 -1.49170929711312 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 476746 4330 516419 -1.49170929711312 "#B80047FF" "healthy cortex cell 445" "GSM1658345" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485929" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996305" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658345/GSM1658345_nochipID4.C21.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996305" "GSM1658345_nochipID4.C21.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -1.28835483692586 -1.28835483692586 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 539566 8031 475496 -1.28835483692586 "#7C0083FF" "healthy cortex cell 446" "GSM1658346" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485930" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996306" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658346/GSM1658346_nochipID4.C33.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996306" "GSM1658346_nochipID4.C33.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 1.28817568387836 1.28817568387836 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 520805 4148 509579 1.28817568387836 "#B4004BFF" "healthy cortex cell 447" "GSM1658347" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485931" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996307" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658347/GSM1658347_nochipID4.C34.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996307" "GSM1658347_nochipID4.C34.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalRep" -0.44 -0.670059810914099 -0.670059810914099 "FB_S6" 1 2 "orange4" 3 21 2 "#FF0000FF" "#000000FF" 559487 7223 675207 -0.670059810914099 "#CE0031FF" "healthy cortex cell 448" "GSM1658348" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485932" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996308" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658348/GSM1658348_nochipID4.C38.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996308" "GSM1658348_nochipID4.C38.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -2.10309108585119 -2.10309108585119 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 772687 5531 544400 -2.10309108585119 "#D60029FF" "healthy cortex cell 449" "GSM1658349" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485933" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996309" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658349/GSM1658349_nochipID4.C39.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996309" "GSM1658349_nochipID4.C39.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -0.0389600904285908 -0.0389600904285908 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 792952 5933 592595 -0.0389600904285908 "#F1000EFF" "healthy cortex cell 450" "GSM1658350" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485934" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996310" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658350/GSM1658350_nochipID4.C41.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996310" "GSM1658350_nochipID4.C41.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -1.46202533185482 -1.46202533185482 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 870554 6027 588922 -1.46202533185482 "#CE0031FF" "healthy cortex cell 451" "GSM1658351" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485926" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996311" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658351/GSM1658351_nochipID4.C42.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996311" "GSM1658351_nochipID4.C42.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 0.537254238910973 0.537254238910973 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 626799 7231 688418 0.537254238910973 "#C3003CFF" "healthy cortex cell 452" "GSM1658352" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485927" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996312" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658352/GSM1658352_nochipID4.C44.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996312" "GSM1658352_nochipID4.C44.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -1.59056299977005 -1.59056299977005 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 678967 7568 662845 -1.59056299977005 "#DA0025FF" "healthy cortex cell 453" "GSM1658353" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485928" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996313" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658353/GSM1658353_nochipID4.C49.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996313" "GSM1658353_nochipID4.C49.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -0.454262068085372 -0.454262068085372 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 796547 7047 623199 -0.454262068085372 "#DC0023FF" "healthy cortex cell 454" "GSM1658354" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485935" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996314" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658354/GSM1658354_nochipID4.C52.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996314" "GSM1658354_nochipID4.C52.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 0.205520035177469 0.205520035177469 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 1013645 4272 690331 0.205520035177469 "#BF0040FF" "healthy cortex cell 455" "GSM1658355" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_replicating" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485894" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996315" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658355/GSM1658355_nochipID4.C53.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996315" "GSM1658355_nochipID4.C53.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalRep" -0.44 0.00732503686100244 0.00732503686100244 "FB_S6" 1 2 "orange4" 3 21 2 "#FF0000FF" "#000000FF" 769610 4413 582172 0.00732503686100244 "#6B0094FF" "healthy cortex cell 456" "GSM1658356" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485895" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996316" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658356/GSM1658356_nochipID4.C59.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996316" "GSM1658356_nochipID4.C59.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -1.71386928815395 -1.71386928815395 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 1034865 8465 625068 -1.71386928815395 "#CE0031FF" "healthy cortex cell 457" "GSM1658357" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485896" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996317" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658357/GSM1658357_nochipID4.C62.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996317" "GSM1658357_nochipID4.C62.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 1.02868218760937 1.02868218760937 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 1136953 7730 601759 1.02868218760937 "#FB0004FF" "healthy cortex cell 458" "GSM1658358" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485897" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996318" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658358/GSM1658358_nochipID4.C63.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996318" "GSM1658358_nochipID4.C63.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -1.00468070857227 -1.00468070857227 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 862137 4973 525037 -1.00468070857227 "#BD0042FF" "healthy cortex cell 459" "GSM1658359" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485898" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996319" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658359/GSM1658359_nochipID4.C66.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996319" "GSM1658359_nochipID4.C66.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 0.734024523235858 0.734024523235858 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 402523 4168 456087 0.734024523235858 "#EA0015FF" "healthy cortex cell 460" "GSM1658360" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485899" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996320" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658360/GSM1658360_nochipID4.C74.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996320" "GSM1658360_nochipID4.C74.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 1.38706473674625 1.38706473674625 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 913528 5718 570485 1.38706473674625 "#B80047FF" "healthy cortex cell 461" "GSM1658361" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485900" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996321" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658361/GSM1658361_nochipID4.C77.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996321" "GSM1658361_nochipID4.C77.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -0.192385308966041 -0.192385308966041 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 592939 5249 466276 -0.192385308966041 "#E1001EFF" "healthy cortex cell 462" "GSM1658362" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485901" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996322" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658362/GSM1658362_nochipID4.C78.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996322" "GSM1658362_nochipID4.C78.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -0.673157356269658 -0.673157356269658 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 505954 5350 465384 -0.673157356269658 "#EC0013FF" "healthy cortex cell 463" "GSM1658363" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485902" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996323" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658363/GSM1658363_nochipID4.C84.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996323" "GSM1658363_nochipID4.C84.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -1.98001944232732 -1.98001944232732 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 750682 7668 655463 -1.98001944232732 "#C90036FF" "healthy cortex cell 464" "GSM1658364" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485903" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996324" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658364/GSM1658364_nochipID4.C89.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996324" "GSM1658364_nochipID4.C89.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 0.927177441716194 0.927177441716194 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 606953 7337 460247 0.927177441716194 "#BA0045FF" "healthy cortex cell 465" "GSM1658365" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485904" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996325" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658365/GSM1658365_nochipID4.C95.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996325" "GSM1658365_nochipID4.C95.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 1.50958236161619 1.50958236161619 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 1063098 8792 830121 1.50958236161619 "#DF0020FF" "healthy cortex cell 466" "GSM1658366" "Public on May 20 2015" "Apr 15 2015" "Jul 02 2015" "SRA" "1" "Brain" "Homo sapiens" "tissue: cortex (temporal lobe)" "cell type: fetal_quiescent" "age: prenatal 16-18 W" "c1 chip id: nochipID4" "experiment_sample_name: FB_S6" "total RNA" "C1 autoprep standard protocol" "C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol" "Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system." "9606" "Single cell from healthy human cortex" "Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1)." "Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif )." "Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no)." "Genome_build: hg19" "Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample" "GPL18573" "Martin,,Enge" "martin.enge@ki.se" "Taipale lab" "Dep of Biosciences and Nutrition, Novum" "Karolinska Institute" "Hälsovägen 7" "Stockholm" "SE-14157" "Sweden" "0" "Illumina NextSeq 500" "cDNA" "transcriptomic" "RNA-Seq" "BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN03485905" "SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX996326" "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1658nnn/GSM1658366/GSM1658366_nochipID4.C96.csv.gz" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996326" "GSM1658366_nochipID4.C96.csv" "Illumina NextSeq 500" "nochipID4" "TemporalLobe" "fetalQui" -0.44 -2.34050440561026 -2.34050440561026 "FB_S6" 1 2 "orange" 4 21 2 "#FF0000FF" "#000000FF" 791301 4359 730874 -2.34050440561026 "#D70028FF"