MartinEnge martin.enge@ki.se Dep of Oncology-Pathology Karolinska Institute

CCK, Z4 Stockholm S-171 76 Sweden

GEO

USA

SpyrosDarmanis StephenRQuake StevenASloan BenABarres YeZhang ChristineCaneda MelanieGHayden Gephart LawrenceMShuer Gene Expression Omnibus (GEO) GEO NCBI NLM NIH http://www.ncbi.nlm.nih.gov/geo geo@ncbi.nlm.nih.gov 2012-05-02 2012-05-02 2017-09-14 GPL15520 high-throughput sequencing virtual Homo sapiens 2014-04-15 2014-04-15 2017-10-06 GPL18573 high-throughput sequencing virtual Homo sapiens 2015-04-15 2015-05-20 2015-11-06 GSM1657871 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657871/suppl/GSM1657871_1772078217.C03.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995861 2015-04-15 2015-05-20 2015-11-06 GSM1657872 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657872/suppl/GSM1657872_1772078217.C04.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995862 2015-04-15 2015-05-20 2015-11-06 GSM1657873 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657873/suppl/GSM1657873_1772078217.C06.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995863 2015-04-15 2015-05-20 2015-11-06 GSM1657874 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657874/suppl/GSM1657874_1772078217.C07.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995864 2015-04-15 2015-05-20 2015-11-06 GSM1657875 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657875/suppl/GSM1657875_1772078217.C08.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995865 2015-04-15 2015-05-20 2015-11-06 GSM1657876 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657876/suppl/GSM1657876_1772078217.C09.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995866 2015-04-15 2015-05-20 2015-11-06 GSM1657877 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657877/suppl/GSM1657877_1772078217.C14.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995867 2015-04-15 2015-05-20 2015-11-06 GSM1657878 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657878/suppl/GSM1657878_1772078217.C16.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995868 2015-04-15 2015-05-20 2015-11-06 GSM1657879 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657879/suppl/GSM1657879_1772078217.C17.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995869 2015-04-15 2015-05-20 2015-11-06 GSM1657880 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657880/suppl/GSM1657880_1772078217.C18.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995870 2015-04-15 2015-05-20 2015-11-06 GSM1657881 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657881/suppl/GSM1657881_1772078217.C20.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995871 2015-04-15 2015-05-20 2015-11-06 GSM1657882 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657882/suppl/GSM1657882_1772078217.C23.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995872 2015-04-15 2015-05-20 2015-11-06 GSM1657883 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657883/suppl/GSM1657883_1772078217.C28.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995873 2015-04-15 2015-05-20 2015-11-06 GSM1657884 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657884/suppl/GSM1657884_1772078217.C29.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995874 2015-04-15 2015-05-20 2015-11-06 GSM1657885 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657885/suppl/GSM1657885_1772078217.C32.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995875 2015-04-15 2015-05-20 2015-11-06 GSM1657886 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657886/suppl/GSM1657886_1772078217.C33.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995876 2015-04-15 2015-05-20 2015-11-06 GSM1657887 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657887/suppl/GSM1657887_1772078217.C39.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995877 2015-04-15 2015-05-20 2015-11-06 GSM1657888 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657888/suppl/GSM1657888_1772078217.C40.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995878 2015-04-15 2015-05-20 2015-11-06 GSM1657889 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657889/suppl/GSM1657889_1772078217.C47.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995879 2015-04-15 2015-05-20 2015-11-06 GSM1657890 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657890/suppl/GSM1657890_1772078217.C52.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995880 2015-04-15 2015-05-20 2015-11-06 GSM1657891 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657891/suppl/GSM1657891_1772078217.C56.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995881 2015-04-15 2015-05-20 2015-11-06 GSM1657892 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657892/suppl/GSM1657892_1772078217.C58.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995882 2015-04-15 2015-05-20 2015-11-06 GSM1657893 SRA 1 Brain Homo sapiens cortex OPC postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657893/suppl/GSM1657893_1772078217.C59.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995883 2015-04-15 2015-05-20 2015-11-06 GSM1657894 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657894/suppl/GSM1657894_1772078217.C60.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995884 2015-04-15 2015-05-20 2015-11-06 GSM1657895 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657895/suppl/GSM1657895_1772078217.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995885 2015-04-15 2015-05-20 2015-11-06 GSM1657896 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657896/suppl/GSM1657896_1772078217.C66.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995886 2015-04-15 2015-05-20 2015-11-06 GSM1657897 SRA 1 Brain Homo sapiens cortex hybrid postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657897/suppl/GSM1657897_1772078217.C72.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995887 2015-04-15 2015-05-20 2015-11-06 GSM1657898 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657898/suppl/GSM1657898_1772078217.C80.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995888 2015-04-15 2015-05-20 2015-11-06 GSM1657899 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657899/suppl/GSM1657899_1772078217.C87.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995889 2015-04-15 2015-05-20 2015-11-06 GSM1657900 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657900/suppl/GSM1657900_1772078217.C89.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995890 2015-04-15 2015-05-20 2015-11-06 GSM1657901 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657901/suppl/GSM1657901_1772078217.C91.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995891 2015-04-15 2015-05-20 2015-11-06 GSM1657902 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657902/suppl/GSM1657902_1772078217.C94.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995892 2015-04-15 2015-05-20 2015-11-06 GSM1657903 SRA 1 Brain Homo sapiens cortex OPC postnatal 54 years 1772078217 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657903/suppl/GSM1657903_1772078217.C96.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995893 2015-04-15 2015-05-20 2015-11-06 GSM1657904 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657904/suppl/GSM1657904_1772078218.C05.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995894 2015-04-15 2015-05-20 2015-11-06 GSM1657905 SRA 1 Brain Homo sapiens hippocampus hybrid postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657905/suppl/GSM1657905_1772078218.C08.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995895 2015-04-15 2015-05-20 2015-11-06 GSM1657906 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657906/suppl/GSM1657906_1772078218.C09.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995896 2015-04-15 2015-05-20 2015-11-06 GSM1657907 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657907/suppl/GSM1657907_1772078218.C13.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995897 2015-04-15 2015-05-20 2015-11-06 GSM1657908 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657908/suppl/GSM1657908_1772078218.C18.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995898 2015-04-15 2015-05-20 2015-11-06 GSM1657909 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657909/suppl/GSM1657909_1772078218.C23.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995899 2015-04-15 2015-05-20 2015-11-06 GSM1657910 SRA 1 Brain Homo sapiens hippocampus microglia postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657910/suppl/GSM1657910_1772078218.C27.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995900 2015-04-15 2015-05-20 2015-11-06 GSM1657911 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657911/suppl/GSM1657911_1772078218.C29.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995901 2015-04-15 2015-05-20 2015-11-06 GSM1657912 SRA 1 Brain Homo sapiens hippocampus hybrid postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657912/suppl/GSM1657912_1772078218.C32.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995902 2015-04-15 2015-05-20 2015-11-06 GSM1657913 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657913/suppl/GSM1657913_1772078218.C34.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995903 2015-04-15 2015-05-20 2015-11-06 GSM1657914 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657914/suppl/GSM1657914_1772078218.C43.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995904 2015-04-15 2015-05-20 2015-11-06 GSM1657915 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657915/suppl/GSM1657915_1772078218.C44.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995905 2015-04-15 2015-05-20 2015-11-06 GSM1657916 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657916/suppl/GSM1657916_1772078218.C47.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995906 2015-04-15 2015-05-20 2015-11-06 GSM1657917 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657917/suppl/GSM1657917_1772078218.C48.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995907 2015-04-15 2015-05-20 2015-11-06 GSM1657918 SRA 1 Brain Homo sapiens hippocampus microglia postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657918/suppl/GSM1657918_1772078218.C53.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995908 2015-04-15 2015-05-20 2015-11-06 GSM1657919 SRA 1 Brain Homo sapiens hippocampus microglia postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657919/suppl/GSM1657919_1772078218.C55.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995909 2015-04-15 2015-05-20 2015-11-06 GSM1657920 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657920/suppl/GSM1657920_1772078218.C56.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995910 2015-04-15 2015-05-20 2015-11-06 GSM1657921 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657921/suppl/GSM1657921_1772078218.C58.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995911 2015-04-15 2015-05-20 2015-11-06 GSM1657922 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657922/suppl/GSM1657922_1772078218.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995912 2015-04-15 2015-05-20 2015-11-06 GSM1657923 SRA 1 Brain Homo sapiens hippocampus microglia postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657923/suppl/GSM1657923_1772078218.C71.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995913 2015-04-15 2015-05-20 2015-11-06 GSM1657924 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657924/suppl/GSM1657924_1772078218.C85.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995914 2015-04-15 2015-05-20 2015-11-06 GSM1657925 SRA 1 Brain Homo sapiens hippocampus microglia postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657925/suppl/GSM1657925_1772078218.C88.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995915 2015-04-15 2015-05-20 2015-11-06 GSM1657926 SRA 1 Brain Homo sapiens hippocampus microglia postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657926/suppl/GSM1657926_1772078218.C89.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995916 2015-04-15 2015-05-20 2015-11-06 GSM1657927 SRA 1 Brain Homo sapiens hippocampus microglia postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657927/suppl/GSM1657927_1772078218.C93.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995917 2015-04-15 2015-05-20 2015-11-06 GSM1657928 SRA 1 Brain Homo sapiens hippocampus OPC postnatal 54 years 1772078218 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657928/suppl/GSM1657928_1772078218.C95.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995918 2015-04-15 2015-05-20 2015-11-06 GSM1657929 SRA 1 Brain Homo sapiens cortex hybrid postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657929/suppl/GSM1657929_1772078236.C11.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995919 2015-04-15 2015-05-20 2015-11-06 GSM1657930 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657930/suppl/GSM1657930_1772078236.C12.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995920 2015-04-15 2015-05-20 2015-11-06 GSM1657931 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657931/suppl/GSM1657931_1772078236.C16.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995921 2015-04-15 2015-05-20 2015-11-06 GSM1657932 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657932/suppl/GSM1657932_1772078236.C17.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995922 2015-04-15 2015-05-20 2015-11-06 GSM1657933 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657933/suppl/GSM1657933_1772078236.C19.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995923 2015-04-15 2015-05-20 2015-11-06 GSM1657934 SRA 1 Brain Homo sapiens cortex microglia postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657934/suppl/GSM1657934_1772078236.C25.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995924 2015-04-15 2015-05-20 2015-11-06 GSM1657935 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657935/suppl/GSM1657935_1772078236.C26.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995925 2015-04-15 2015-05-20 2015-11-06 GSM1657936 SRA 1 Brain Homo sapiens cortex hybrid postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657936/suppl/GSM1657936_1772078236.C27.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995926 2015-04-15 2015-05-20 2015-11-06 GSM1657937 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657937/suppl/GSM1657937_1772078236.C28.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995927 2015-04-15 2015-05-20 2015-11-06 GSM1657938 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657938/suppl/GSM1657938_1772078236.C30.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995928 2015-04-15 2015-05-20 2015-11-06 GSM1657939 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657939/suppl/GSM1657939_1772078236.C31.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995929 2015-04-15 2015-05-20 2015-11-06 GSM1657940 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657940/suppl/GSM1657940_1772078236.C32.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995930 2015-04-15 2015-05-20 2015-11-06 GSM1657941 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657941/suppl/GSM1657941_1772078236.C33.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995931 2015-04-15 2015-05-20 2015-11-06 GSM1657942 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657942/suppl/GSM1657942_1772078236.C34.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995932 2015-04-15 2015-05-20 2015-11-06 GSM1657943 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657943/suppl/GSM1657943_1772078236.C36.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995933 2015-04-15 2015-05-20 2015-11-06 GSM1657944 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657944/suppl/GSM1657944_1772078236.C38.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995934 2015-04-15 2015-05-20 2015-11-06 GSM1657945 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657945/suppl/GSM1657945_1772078236.C40.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995935 2015-04-15 2015-05-20 2015-11-06 GSM1657946 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657946/suppl/GSM1657946_1772078236.C41.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995936 2015-04-15 2015-05-20 2015-11-06 GSM1657947 SRA 1 Brain Homo sapiens cortex hybrid postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657947/suppl/GSM1657947_1772078236.C45.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995937 2015-04-15 2015-05-20 2015-11-06 GSM1657948 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657948/suppl/GSM1657948_1772078236.C46.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995938 2015-04-15 2015-05-20 2015-11-06 GSM1657949 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657949/suppl/GSM1657949_1772078236.C47.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995939 2015-04-15 2015-05-20 2015-11-06 GSM1657950 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657950/suppl/GSM1657950_1772078236.C49.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995940 2015-04-15 2015-05-20 2015-11-06 GSM1657951 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657951/suppl/GSM1657951_1772078236.C54.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995941 2015-04-15 2015-05-20 2015-11-06 GSM1657952 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657952/suppl/GSM1657952_1772078236.C56.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995942 2015-04-15 2015-05-20 2015-11-06 GSM1657953 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657953/suppl/GSM1657953_1772078236.C57.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995943 2015-04-15 2015-05-20 2015-11-06 GSM1657954 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657954/suppl/GSM1657954_1772078236.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995944 2015-04-15 2015-05-20 2015-11-06 GSM1657955 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657955/suppl/GSM1657955_1772078236.C65.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995945 2015-04-15 2015-05-20 2015-11-06 GSM1657956 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657956/suppl/GSM1657956_1772078236.C66.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995946 2015-04-15 2015-05-20 2015-11-06 GSM1657957 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657957/suppl/GSM1657957_1772078236.C70.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995947 2015-04-15 2015-05-20 2015-11-06 GSM1657958 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657958/suppl/GSM1657958_1772078236.C74.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995948 2015-04-15 2015-05-20 2015-11-06 GSM1657959 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657959/suppl/GSM1657959_1772078236.C77.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995949 2015-04-15 2015-05-20 2015-11-06 GSM1657960 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657960/suppl/GSM1657960_1772078236.C89.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995950 2015-04-15 2015-05-20 2015-11-06 GSM1657961 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657961/suppl/GSM1657961_1772078236.C90.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995951 2015-04-15 2015-05-20 2015-11-06 GSM1657962 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078236 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657962/suppl/GSM1657962_1772078236.C93.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995952 2015-04-15 2015-05-20 2015-11-06 GSM1657963 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657963/suppl/GSM1657963_1772078237.C06.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995953 2015-04-15 2015-05-20 2015-11-06 GSM1657964 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657964/suppl/GSM1657964_1772078237.C08.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995954 2015-04-15 2015-05-20 2015-11-06 GSM1657965 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657965/suppl/GSM1657965_1772078237.C11.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995955 2015-04-15 2015-05-20 2015-11-06 GSM1657966 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657966/suppl/GSM1657966_1772078237.C13.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995956 2015-04-15 2015-05-20 2015-11-06 GSM1657967 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657967/suppl/GSM1657967_1772078237.C14.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995957 2015-04-15 2015-05-20 2015-11-06 GSM1657968 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657968/suppl/GSM1657968_1772078237.C15.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995958 2015-04-15 2015-05-20 2015-11-06 GSM1657969 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657969/suppl/GSM1657969_1772078237.C19.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995959 2015-04-15 2015-05-20 2015-11-06 GSM1657970 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657970/suppl/GSM1657970_1772078237.C21.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995960 2015-04-15 2015-05-20 2015-11-06 GSM1657971 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657971/suppl/GSM1657971_1772078237.C26.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995961 2015-04-15 2015-05-20 2015-11-06 GSM1657972 SRA 1 Brain Homo sapiens cortex endothelial postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657972/suppl/GSM1657972_1772078237.C28.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995962 2015-04-15 2015-05-20 2015-11-06 GSM1657973 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657973/suppl/GSM1657973_1772078237.C29.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995963 2015-04-15 2015-05-20 2015-11-06 GSM1657974 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657974/suppl/GSM1657974_1772078237.C31.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995964 2015-04-15 2015-05-20 2015-11-06 GSM1657975 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657975/suppl/GSM1657975_1772078237.C40.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995965 2015-04-15 2015-05-20 2015-11-06 GSM1657976 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657976/suppl/GSM1657976_1772078237.C42.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995966 2015-04-15 2015-05-20 2015-11-06 GSM1657977 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657977/suppl/GSM1657977_1772078237.C44.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995967 2015-04-15 2015-05-20 2015-11-06 GSM1657978 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657978/suppl/GSM1657978_1772078237.C47.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995968 2015-04-15 2015-05-20 2015-11-06 GSM1657979 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657979/suppl/GSM1657979_1772078237.C49.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995969 2015-04-15 2015-05-20 2015-11-06 GSM1657980 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657980/suppl/GSM1657980_1772078237.C52.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995970 2015-04-15 2015-05-20 2015-11-06 GSM1657981 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657981/suppl/GSM1657981_1772078237.C55.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995971 2015-04-15 2015-05-20 2015-11-06 GSM1657982 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657982/suppl/GSM1657982_1772078237.C56.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995972 2015-04-15 2015-05-20 2015-11-06 GSM1657983 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657983/suppl/GSM1657983_1772078237.C58.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995973 2015-04-15 2015-05-20 2015-11-06 GSM1657984 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657984/suppl/GSM1657984_1772078237.C60.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995974 2015-04-15 2015-05-20 2015-11-06 GSM1657985 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657985/suppl/GSM1657985_1772078237.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995975 2015-04-15 2015-05-20 2015-11-06 GSM1657986 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657986/suppl/GSM1657986_1772078237.C62.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995976 2015-04-15 2015-05-20 2015-11-06 GSM1657987 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657987/suppl/GSM1657987_1772078237.C74.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995977 2015-04-15 2015-05-20 2015-11-06 GSM1657988 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657988/suppl/GSM1657988_1772078237.C79.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995978 2015-04-15 2015-05-20 2015-11-06 GSM1657989 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657989/suppl/GSM1657989_1772078237.C83.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995979 2015-04-15 2015-05-20 2015-11-06 GSM1657990 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657990/suppl/GSM1657990_1772078237.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995980 2015-04-15 2015-05-20 2015-11-06 GSM1657991 SRA 1 Brain Homo sapiens cortex neurons postnatal 37 years 1772078237 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657991/suppl/GSM1657991_1772078237.C92.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995981 2015-04-15 2015-05-20 2015-11-06 GSM1657992 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID12 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657992/suppl/GSM1657992_nochipID12.C05.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995982 2015-04-15 2015-05-20 2015-11-06 GSM1657993 SRA 1 Brain Homo sapiens cortex endothelial postnatal 47 years nochipID12 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657993/suppl/GSM1657993_nochipID12.C23.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995983 2015-04-15 2015-05-20 2015-11-06 GSM1657994 SRA 1 Brain Homo sapiens cortex microglia postnatal 47 years nochipID12 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657994/suppl/GSM1657994_nochipID12.C73.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995984 2015-04-15 2015-05-20 2015-11-06 GSM1657995 SRA 1 Brain Homo sapiens cortex endothelial postnatal 47 years nochipID12 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657995/suppl/GSM1657995_nochipID12.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995985 2015-04-15 2015-05-20 2015-11-06 GSM1657996 SRA 1 Brain Homo sapiens cortex microglia postnatal 47 years nochipID12 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657996/suppl/GSM1657996_nochipID12.C87.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995986 2015-04-15 2015-05-20 2015-11-06 GSM1657997 SRA 1 Brain Homo sapiens cortex microglia postnatal 63 years nochipID14 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657997/suppl/GSM1657997_nochipID14.C08.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995987 2015-04-15 2015-05-20 2015-11-06 GSM1657998 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 63 years nochipID14 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657998/suppl/GSM1657998_nochipID14.C13.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995988 2015-04-15 2015-05-20 2015-11-06 GSM1657999 SRA 1 Brain Homo sapiens cortex microglia postnatal 63 years nochipID14 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1657nnn/GSM1657999/suppl/GSM1657999_nochipID14.C29.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995989 2015-04-15 2015-05-20 2015-11-06 GSM1658000 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 63 years nochipID14 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658000/suppl/GSM1658000_nochipID14.C45.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995990 2015-04-15 2015-05-20 2015-11-06 GSM1658001 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID14 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658001/suppl/GSM1658001_nochipID14.C89.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995991 2015-04-15 2015-05-20 2015-11-06 GSM1658002 SRA 1 Brain Homo sapiens cortex neurons postnatal 22 years nochipID15 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658002/suppl/GSM1658002_nochipID15.C20.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995992 2015-04-15 2015-05-20 2015-11-06 GSM1658003 SRA 1 Brain Homo sapiens cortex fetal_quiescent postnatal 22 years nochipID15 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658003/suppl/GSM1658003_nochipID15.C54.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995993 2015-04-15 2015-05-20 2015-11-06 GSM1658004 SRA 1 Brain Homo sapiens cortex endothelial postnatal 22 years nochipID15 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658004/suppl/GSM1658004_nochipID15.C69.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995994 2015-04-15 2015-05-20 2015-11-06 GSM1658005 SRA 1 Brain Homo sapiens cortex neurons postnatal 22 years nochipID15 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658005/suppl/GSM1658005_nochipID15.C86.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995995 2015-04-15 2015-05-20 2015-11-06 GSM1658006 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658006/suppl/GSM1658006_nochipID2.C01.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995996 2015-04-15 2015-05-20 2015-11-06 GSM1658007 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658007/suppl/GSM1658007_nochipID2.C02.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995997 2015-04-15 2015-05-20 2015-11-06 GSM1658008 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658008/suppl/GSM1658008_nochipID2.C03.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995998 2015-04-15 2015-05-20 2015-11-06 GSM1658009 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658009/suppl/GSM1658009_nochipID2.C07.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX995/SRX995999 2015-04-15 2015-05-20 2015-11-06 GSM1658010 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658010/suppl/GSM1658010_nochipID2.C08.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996000 2015-04-15 2015-05-20 2015-11-06 GSM1658011 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658011/suppl/GSM1658011_nochipID2.C09.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996001 2015-04-15 2015-05-20 2015-11-06 GSM1658012 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658012/suppl/GSM1658012_nochipID2.C10.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996002 2015-04-15 2015-05-20 2015-11-06 GSM1658013 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658013/suppl/GSM1658013_nochipID2.C11.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996003 2015-04-15 2015-05-20 2015-11-06 GSM1658014 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658014/suppl/GSM1658014_nochipID2.C12.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996004 2015-04-15 2015-05-20 2015-11-06 GSM1658015 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658015/suppl/GSM1658015_nochipID2.C13.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996005 2015-04-15 2015-05-20 2015-11-06 GSM1658016 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658016/suppl/GSM1658016_nochipID2.C14.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996006 2015-04-15 2015-05-20 2015-11-06 GSM1658017 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658017/suppl/GSM1658017_nochipID2.C15.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996007 2015-04-15 2015-05-20 2015-11-06 GSM1658018 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658018/suppl/GSM1658018_nochipID2.C16.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996008 2015-04-15 2015-05-20 2015-11-06 GSM1658019 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658019/suppl/GSM1658019_nochipID2.C17.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996009 2015-04-15 2015-05-20 2015-11-06 GSM1658020 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658020/suppl/GSM1658020_nochipID2.C18.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996010 2015-04-15 2015-05-20 2015-11-06 GSM1658021 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658021/suppl/GSM1658021_nochipID2.C19.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996011 2015-04-15 2015-05-20 2015-11-06 GSM1658022 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658022/suppl/GSM1658022_nochipID2.C21.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996012 2015-04-15 2015-05-20 2015-11-06 GSM1658023 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658023/suppl/GSM1658023_nochipID2.C22.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996013 2015-04-15 2015-05-20 2015-11-06 GSM1658024 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658024/suppl/GSM1658024_nochipID2.C24.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996014 2015-04-15 2015-05-20 2015-11-06 GSM1658025 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658025/suppl/GSM1658025_nochipID2.C26.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996015 2015-04-15 2015-05-20 2015-11-06 GSM1658026 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658026/suppl/GSM1658026_nochipID2.C27.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996016 2015-04-15 2015-05-20 2015-11-06 GSM1658027 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658027/suppl/GSM1658027_nochipID2.C28.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996017 2015-04-15 2015-05-20 2015-11-06 GSM1658028 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658028/suppl/GSM1658028_nochipID2.C29.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996018 2015-04-15 2015-05-20 2015-11-06 GSM1658029 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658029/suppl/GSM1658029_nochipID2.C30.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996019 2015-04-15 2015-05-20 2015-11-06 GSM1658030 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658030/suppl/GSM1658030_nochipID2.C31.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996020 2015-04-15 2015-05-20 2015-11-06 GSM1658031 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658031/suppl/GSM1658031_nochipID2.C32.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996021 2015-04-15 2015-05-20 2015-11-06 GSM1658032 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658032/suppl/GSM1658032_nochipID2.C33.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996022 2015-04-15 2015-05-20 2015-11-06 GSM1658033 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658033/suppl/GSM1658033_nochipID2.C34.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996023 2015-04-15 2015-05-20 2015-11-06 GSM1658034 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658034/suppl/GSM1658034_nochipID2.C36.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996024 2015-04-15 2015-05-20 2015-11-06 GSM1658035 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658035/suppl/GSM1658035_nochipID2.C38.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996025 2015-04-15 2015-05-20 2015-11-06 GSM1658036 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658036/suppl/GSM1658036_nochipID2.C39.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996026 2015-04-15 2015-05-20 2015-11-06 GSM1658037 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658037/suppl/GSM1658037_nochipID2.C40.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996027 2015-04-15 2015-05-20 2015-11-06 GSM1658038 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658038/suppl/GSM1658038_nochipID2.C41.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996028 2015-04-15 2015-05-20 2015-11-06 GSM1658039 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658039/suppl/GSM1658039_nochipID2.C42.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996029 2015-04-15 2015-05-20 2015-11-06 GSM1658040 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658040/suppl/GSM1658040_nochipID2.C43.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996030 2015-04-15 2015-05-20 2015-11-06 GSM1658041 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658041/suppl/GSM1658041_nochipID2.C44.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996031 2015-04-15 2015-05-20 2015-11-06 GSM1658042 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658042/suppl/GSM1658042_nochipID2.C45.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996032 2015-04-15 2015-05-20 2015-11-06 GSM1658043 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658043/suppl/GSM1658043_nochipID2.C46.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996033 2015-04-15 2015-05-20 2015-11-06 GSM1658044 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658044/suppl/GSM1658044_nochipID2.C47.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996034 2015-04-15 2015-05-20 2015-11-06 GSM1658045 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658045/suppl/GSM1658045_nochipID2.C48.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996035 2015-04-15 2015-05-20 2015-11-06 GSM1658046 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658046/suppl/GSM1658046_nochipID2.C49.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996036 2015-04-15 2015-05-20 2015-11-06 GSM1658047 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658047/suppl/GSM1658047_nochipID2.C50.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996037 2015-04-15 2015-05-20 2015-11-06 GSM1658048 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658048/suppl/GSM1658048_nochipID2.C51.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996038 2015-04-15 2015-05-20 2015-11-06 GSM1658049 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658049/suppl/GSM1658049_nochipID2.C52.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996039 2015-04-15 2015-05-20 2015-11-06 GSM1658050 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658050/suppl/GSM1658050_nochipID2.C56.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996040 2015-04-15 2015-05-20 2015-11-06 GSM1658051 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658051/suppl/GSM1658051_nochipID2.C57.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996041 2015-04-15 2015-05-20 2015-11-06 GSM1658052 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658052/suppl/GSM1658052_nochipID2.C58.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996042 2015-04-15 2015-05-20 2015-11-06 GSM1658053 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658053/suppl/GSM1658053_nochipID2.C59.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996043 2015-04-15 2015-05-20 2015-11-06 GSM1658054 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658054/suppl/GSM1658054_nochipID2.C60.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996044 2015-04-15 2015-05-20 2015-11-06 GSM1658055 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658055/suppl/GSM1658055_nochipID2.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996045 2015-04-15 2015-05-20 2015-11-06 GSM1658056 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658056/suppl/GSM1658056_nochipID2.C62.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996046 2015-04-15 2015-05-20 2015-11-06 GSM1658057 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658057/suppl/GSM1658057_nochipID2.C63.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996047 2015-04-15 2015-05-20 2015-11-06 GSM1658058 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658058/suppl/GSM1658058_nochipID2.C64.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996048 2015-04-15 2015-05-20 2015-11-06 GSM1658059 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658059/suppl/GSM1658059_nochipID2.C65.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996049 2015-04-15 2015-05-20 2015-11-06 GSM1658060 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658060/suppl/GSM1658060_nochipID2.C66.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996050 2015-04-15 2015-05-20 2015-11-06 GSM1658061 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658061/suppl/GSM1658061_nochipID2.C67.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996051 2015-04-15 2015-05-20 2015-11-06 GSM1658062 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658062/suppl/GSM1658062_nochipID2.C68.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996052 2015-04-15 2015-05-20 2015-11-06 GSM1658063 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658063/suppl/GSM1658063_nochipID2.C69.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996053 2015-04-15 2015-05-20 2015-11-06 GSM1658064 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658064/suppl/GSM1658064_nochipID2.C71.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996054 2015-04-15 2015-05-20 2015-11-06 GSM1658065 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658065/suppl/GSM1658065_nochipID2.C73.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996055 2015-04-15 2015-05-20 2015-11-06 GSM1658066 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658066/suppl/GSM1658066_nochipID2.C75.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996056 2015-04-15 2015-05-20 2015-11-06 GSM1658067 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658067/suppl/GSM1658067_nochipID2.C76.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996057 2015-04-15 2015-05-20 2015-11-06 GSM1658068 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658068/suppl/GSM1658068_nochipID2.C77.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996058 2015-04-15 2015-05-20 2015-11-06 GSM1658069 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658069/suppl/GSM1658069_nochipID2.C78.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996059 2015-04-15 2015-05-20 2015-11-06 GSM1658070 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658070/suppl/GSM1658070_nochipID2.C79.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996060 2015-04-15 2015-05-20 2015-11-06 GSM1658071 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658071/suppl/GSM1658071_nochipID2.C80.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996061 2015-04-15 2015-05-20 2015-11-06 GSM1658072 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658072/suppl/GSM1658072_nochipID2.C81.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996062 2015-04-15 2015-05-20 2015-11-06 GSM1658073 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658073/suppl/GSM1658073_nochipID2.C82.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996063 2015-04-15 2015-05-20 2015-11-06 GSM1658074 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658074/suppl/GSM1658074_nochipID2.C83.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996064 2015-04-15 2015-05-20 2015-11-06 GSM1658075 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658075/suppl/GSM1658075_nochipID2.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996065 2015-04-15 2015-05-20 2015-11-06 GSM1658076 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658076/suppl/GSM1658076_nochipID2.C85.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996066 2015-04-15 2015-05-20 2015-11-06 GSM1658077 SRA 1 Brain Homo sapiens cortex hybrid postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658077/suppl/GSM1658077_nochipID2.C86.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996067 2015-04-15 2015-05-20 2015-11-06 GSM1658078 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658078/suppl/GSM1658078_nochipID2.C87.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996068 2015-04-15 2015-05-20 2015-11-06 GSM1658079 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658079/suppl/GSM1658079_nochipID2.C89.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996069 2015-04-15 2015-05-20 2015-11-06 GSM1658080 SRA 1 Brain Homo sapiens cortex neurons postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658080/suppl/GSM1658080_nochipID2.C90.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996070 2015-04-15 2015-05-20 2015-11-06 GSM1658081 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658081/suppl/GSM1658081_nochipID2.C92.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996071 2015-04-15 2015-05-20 2015-11-06 GSM1658082 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 50 years nochipID2 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658082/suppl/GSM1658082_nochipID2.C93.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996072 2015-04-15 2015-05-20 2015-11-06 GSM1658083 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658083/suppl/GSM1658083_nochipID3.C01.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996073 2015-04-15 2015-05-20 2015-11-06 GSM1658084 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658084/suppl/GSM1658084_nochipID3.C05.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996074 2015-04-15 2015-05-20 2015-11-06 GSM1658085 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658085/suppl/GSM1658085_nochipID3.C06.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996075 2015-04-15 2015-05-20 2015-11-06 GSM1658086 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658086/suppl/GSM1658086_nochipID3.C07.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996076 2015-04-15 2015-05-20 2015-11-06 GSM1658087 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658087/suppl/GSM1658087_nochipID3.C09.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996077 2015-04-15 2015-05-20 2015-11-06 GSM1658088 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658088/suppl/GSM1658088_nochipID3.C11.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996078 2015-04-15 2015-05-20 2015-11-06 GSM1658089 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658089/suppl/GSM1658089_nochipID3.C12.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996079 2015-04-15 2015-05-20 2015-11-06 GSM1658090 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658090/suppl/GSM1658090_nochipID3.C14.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996080 2015-04-15 2015-05-20 2015-11-06 GSM1658091 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658091/suppl/GSM1658091_nochipID3.C23.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996081 2015-04-15 2015-05-20 2015-11-06 GSM1658092 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658092/suppl/GSM1658092_nochipID3.C25.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996082 2015-04-15 2015-05-20 2015-11-06 GSM1658093 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658093/suppl/GSM1658093_nochipID3.C32.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996083 2015-04-15 2015-05-20 2015-11-06 GSM1658094 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658094/suppl/GSM1658094_nochipID3.C37.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996084 2015-04-15 2015-05-20 2015-11-06 GSM1658095 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658095/suppl/GSM1658095_nochipID3.C38.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996085 2015-04-15 2015-05-20 2015-11-06 GSM1658096 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658096/suppl/GSM1658096_nochipID3.C51.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996086 2015-04-15 2015-05-20 2015-11-06 GSM1658097 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658097/suppl/GSM1658097_nochipID3.C52.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996087 2015-04-15 2015-05-20 2015-11-06 GSM1658098 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658098/suppl/GSM1658098_nochipID3.C53.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996088 2015-04-15 2015-05-20 2015-11-06 GSM1658099 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658099/suppl/GSM1658099_nochipID3.C54.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996089 2015-04-15 2015-05-20 2015-11-06 GSM1658100 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658100/suppl/GSM1658100_nochipID3.C56.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996090 2015-04-15 2015-05-20 2015-11-06 GSM1658101 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658101/suppl/GSM1658101_nochipID3.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996091 2015-04-15 2015-05-20 2015-11-06 GSM1658102 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658102/suppl/GSM1658102_nochipID3.C62.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996092 2015-04-15 2015-05-20 2015-11-06 GSM1658103 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658103/suppl/GSM1658103_nochipID3.C65.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996093 2015-04-15 2015-05-20 2015-11-06 GSM1658104 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658104/suppl/GSM1658104_nochipID3.C69.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996094 2015-04-15 2015-05-20 2015-11-06 GSM1658105 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658105/suppl/GSM1658105_nochipID3.C71.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996095 2015-04-15 2015-05-20 2015-11-06 GSM1658106 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658106/suppl/GSM1658106_nochipID3.C72.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996096 2015-04-15 2015-05-20 2015-11-06 GSM1658107 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658107/suppl/GSM1658107_nochipID3.C74.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996097 2015-04-15 2015-05-20 2015-11-06 GSM1658108 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658108/suppl/GSM1658108_nochipID3.C75.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996098 2015-04-15 2015-05-20 2015-11-06 GSM1658109 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658109/suppl/GSM1658109_nochipID3.C76.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996099 2015-04-15 2015-05-20 2015-11-06 GSM1658110 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658110/suppl/GSM1658110_nochipID3.C80.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996100 2015-04-15 2015-05-20 2015-11-06 GSM1658111 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658111/suppl/GSM1658111_nochipID3.C81.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996101 2015-04-15 2015-05-20 2015-11-06 GSM1658112 SRA 1 Brain Homo sapiens cortex endothelial postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658112/suppl/GSM1658112_nochipID3.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996102 2015-04-15 2015-05-20 2015-11-06 GSM1658113 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658113/suppl/GSM1658113_nochipID3.C85.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996103 2015-04-15 2015-05-20 2015-11-06 GSM1658114 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658114/suppl/GSM1658114_nochipID3.C86.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996104 2015-04-15 2015-05-20 2015-11-06 GSM1658115 SRA 1 Brain Homo sapiens cortex neurons postnatal 63 years nochipID3 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658115/suppl/GSM1658115_nochipID3.C91.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996105 2015-04-15 2015-05-20 2015-11-06 GSM1658116 SRA 1 Brain Homo sapiens hippocampus microglia postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658116/suppl/GSM1658116_nochipID5.C04.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996106 2015-04-15 2015-05-20 2015-11-06 GSM1658117 SRA 1 Brain Homo sapiens hippocampus endothelial postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658117/suppl/GSM1658117_nochipID5.C05.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996107 2015-04-15 2015-05-20 2015-11-06 GSM1658118 SRA 1 Brain Homo sapiens hippocampus oligodendrocytes postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658118/suppl/GSM1658118_nochipID5.C18.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996108 2015-04-15 2015-05-20 2015-11-06 GSM1658119 SRA 1 Brain Homo sapiens hippocampus oligodendrocytes postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658119/suppl/GSM1658119_nochipID5.C19.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996109 2015-04-15 2015-05-20 2015-11-06 GSM1658120 SRA 1 Brain Homo sapiens hippocampus oligodendrocytes postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658120/suppl/GSM1658120_nochipID5.C42.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996110 2015-04-15 2015-05-20 2015-11-06 GSM1658121 SRA 1 Brain Homo sapiens hippocampus neurons postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658121/suppl/GSM1658121_nochipID5.C44.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996111 2015-04-15 2015-05-20 2015-11-06 GSM1658122 SRA 1 Brain Homo sapiens hippocampus endothelial postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658122/suppl/GSM1658122_nochipID5.C45.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996112 2015-04-15 2015-05-20 2015-11-06 GSM1658123 SRA 1 Brain Homo sapiens hippocampus oligodendrocytes postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658123/suppl/GSM1658123_nochipID5.C54.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996113 2015-04-15 2015-05-20 2015-11-06 GSM1658124 SRA 1 Brain Homo sapiens hippocampus oligodendrocytes postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658124/suppl/GSM1658124_nochipID5.C65.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996114 2015-04-15 2015-05-20 2015-11-06 GSM1658125 SRA 1 Brain Homo sapiens hippocampus oligodendrocytes postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658125/suppl/GSM1658125_nochipID5.C72.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996115 2015-04-15 2015-05-20 2015-11-06 GSM1658126 SRA 1 Brain Homo sapiens hippocampus endothelial postnatal 63 years nochipID5 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658126/suppl/GSM1658126_nochipID5.C91.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996116 2015-04-15 2015-05-20 2015-11-06 GSM1658127 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658127/suppl/GSM1658127_nochipID8.C01.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996117 2015-04-15 2015-05-20 2015-11-06 GSM1658128 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658128/suppl/GSM1658128_nochipID8.C02.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996118 2015-04-15 2015-05-20 2015-11-06 GSM1658129 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658129/suppl/GSM1658129_nochipID8.C05.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996119 2015-04-15 2015-05-20 2015-11-06 GSM1658130 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658130/suppl/GSM1658130_nochipID8.C06.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996120 2015-04-15 2015-05-20 2015-11-06 GSM1658131 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658131/suppl/GSM1658131_nochipID8.C08.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996121 2015-04-15 2015-05-20 2015-11-06 GSM1658132 SRA 1 Brain Homo sapiens cortex hybrid postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658132/suppl/GSM1658132_nochipID8.C11.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996122 2015-04-15 2015-05-20 2015-11-06 GSM1658133 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658133/suppl/GSM1658133_nochipID8.C12.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996123 2015-04-15 2015-05-20 2015-11-06 GSM1658134 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658134/suppl/GSM1658134_nochipID8.C13.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996124 2015-04-15 2015-05-20 2015-11-06 GSM1658135 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658135/suppl/GSM1658135_nochipID8.C14.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996125 2015-04-15 2015-05-20 2015-11-06 GSM1658136 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658136/suppl/GSM1658136_nochipID8.C17.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996126 2015-04-15 2015-05-20 2015-11-06 GSM1658137 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658137/suppl/GSM1658137_nochipID8.C19.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996127 2015-04-15 2015-05-20 2015-11-06 GSM1658138 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658138/suppl/GSM1658138_nochipID8.C20.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996128 2015-04-15 2015-05-20 2015-11-06 GSM1658139 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658139/suppl/GSM1658139_nochipID8.C22.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996129 2015-04-15 2015-05-20 2015-11-06 GSM1658140 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658140/suppl/GSM1658140_nochipID8.C23.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996130 2015-04-15 2015-05-20 2015-11-06 GSM1658141 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658141/suppl/GSM1658141_nochipID8.C25.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996131 2015-04-15 2015-05-20 2015-11-06 GSM1658142 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658142/suppl/GSM1658142_nochipID8.C28.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996132 2015-04-15 2015-05-20 2015-11-06 GSM1658143 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658143/suppl/GSM1658143_nochipID8.C29.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996133 2015-04-15 2015-05-20 2015-11-06 GSM1658144 SRA 1 Brain Homo sapiens cortex hybrid postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658144/suppl/GSM1658144_nochipID8.C30.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996134 2015-04-15 2015-05-20 2015-11-06 GSM1658145 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658145/suppl/GSM1658145_nochipID8.C32.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996135 2015-04-15 2015-05-20 2015-11-06 GSM1658146 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658146/suppl/GSM1658146_nochipID8.C36.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996136 2015-04-15 2015-05-20 2015-11-06 GSM1658147 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658147/suppl/GSM1658147_nochipID8.C37.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996137 2015-04-15 2015-05-20 2015-11-06 GSM1658148 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658148/suppl/GSM1658148_nochipID8.C39.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996138 2015-04-15 2015-05-20 2015-11-06 GSM1658149 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658149/suppl/GSM1658149_nochipID8.C40.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996139 2015-04-15 2015-05-20 2015-11-06 GSM1658150 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658150/suppl/GSM1658150_nochipID8.C41.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996140 2015-04-15 2015-05-20 2015-11-06 GSM1658151 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658151/suppl/GSM1658151_nochipID8.C42.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996141 2015-04-15 2015-05-20 2015-11-06 GSM1658152 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658152/suppl/GSM1658152_nochipID8.C43.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996142 2015-04-15 2015-05-20 2015-11-06 GSM1658153 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658153/suppl/GSM1658153_nochipID8.C45.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996143 2015-04-15 2015-05-20 2015-11-06 GSM1658154 SRA 1 Brain Homo sapiens cortex hybrid postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658154/suppl/GSM1658154_nochipID8.C48.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996144 2015-04-15 2015-05-20 2015-11-06 GSM1658155 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658155/suppl/GSM1658155_nochipID8.C49.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996145 2015-04-15 2015-05-20 2015-11-06 GSM1658156 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658156/suppl/GSM1658156_nochipID8.C50.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996146 2015-04-15 2015-05-20 2015-11-06 GSM1658157 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658157/suppl/GSM1658157_nochipID8.C52.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996147 2015-04-15 2015-05-20 2015-11-06 GSM1658158 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658158/suppl/GSM1658158_nochipID8.C53.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996148 2015-04-15 2015-05-20 2015-11-06 GSM1658159 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658159/suppl/GSM1658159_nochipID8.C54.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996149 2015-04-15 2015-05-20 2015-11-06 GSM1658160 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658160/suppl/GSM1658160_nochipID8.C55.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996150 2015-04-15 2015-05-20 2015-11-06 GSM1658161 SRA 1 Brain Homo sapiens cortex hybrid postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658161/suppl/GSM1658161_nochipID8.C56.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996151 2015-04-15 2015-05-20 2015-11-06 GSM1658162 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658162/suppl/GSM1658162_nochipID8.C57.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996152 2015-04-15 2015-05-20 2015-11-06 GSM1658163 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658163/suppl/GSM1658163_nochipID8.C60.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996153 2015-04-15 2015-05-20 2015-11-06 GSM1658164 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658164/suppl/GSM1658164_nochipID8.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996154 2015-04-15 2015-05-20 2015-11-06 GSM1658165 SRA 1 Brain Homo sapiens cortex hybrid postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658165/suppl/GSM1658165_nochipID8.C64.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996155 2015-04-15 2015-05-20 2015-11-06 GSM1658166 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658166/suppl/GSM1658166_nochipID8.C65.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996156 2015-04-15 2015-05-20 2015-11-06 GSM1658167 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658167/suppl/GSM1658167_nochipID8.C66.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996157 2015-04-15 2015-05-20 2015-11-06 GSM1658168 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658168/suppl/GSM1658168_nochipID8.C67.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996158 2015-04-15 2015-05-20 2015-11-06 GSM1658169 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658169/suppl/GSM1658169_nochipID8.C70.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996159 2015-04-15 2015-05-20 2015-11-06 GSM1658170 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658170/suppl/GSM1658170_nochipID8.C75.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996160 2015-04-15 2015-05-20 2015-11-06 GSM1658171 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658171/suppl/GSM1658171_nochipID8.C77.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996161 2015-04-15 2015-05-20 2015-11-06 GSM1658172 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658172/suppl/GSM1658172_nochipID8.C78.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996162 2015-04-15 2015-05-20 2015-11-06 GSM1658173 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658173/suppl/GSM1658173_nochipID8.C79.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996163 2015-04-15 2015-05-20 2015-11-06 GSM1658174 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658174/suppl/GSM1658174_nochipID8.C81.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996164 2015-04-15 2015-05-20 2015-11-06 GSM1658175 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658175/suppl/GSM1658175_nochipID8.C82.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996165 2015-04-15 2015-05-20 2015-11-06 GSM1658176 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658176/suppl/GSM1658176_nochipID8.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996166 2015-04-15 2015-05-20 2015-11-06 GSM1658177 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658177/suppl/GSM1658177_nochipID8.C85.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996167 2015-04-15 2015-05-20 2015-11-06 GSM1658178 SRA 1 Brain Homo sapiens cortex hybrid postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658178/suppl/GSM1658178_nochipID8.C87.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996168 2015-04-15 2015-05-20 2015-11-06 GSM1658179 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658179/suppl/GSM1658179_nochipID8.C88.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996169 2015-04-15 2015-05-20 2015-11-06 GSM1658180 SRA 1 Brain Homo sapiens cortex oligodendrocytes postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658180/suppl/GSM1658180_nochipID8.C90.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996170 2015-04-15 2015-05-20 2015-11-06 GSM1658181 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658181/suppl/GSM1658181_nochipID8.C92.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996171 2015-04-15 2015-05-20 2015-11-06 GSM1658182 SRA 1 Brain Homo sapiens cortex neurons postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658182/suppl/GSM1658182_nochipID8.C95.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996172 2015-04-15 2015-05-20 2015-11-06 GSM1658183 SRA 1 Brain Homo sapiens cortex hybrid postnatal 21 years nochipID8 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658183/suppl/GSM1658183_nochipID8.C96.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996173 2015-04-15 2015-05-20 2015-11-06 GSM1658184 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658184/suppl/GSM1658184_nochipID9.C01.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996174 2015-04-15 2015-05-20 2015-11-06 GSM1658185 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658185/suppl/GSM1658185_nochipID9.C02.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996175 2015-04-15 2015-05-20 2015-11-06 GSM1658186 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658186/suppl/GSM1658186_nochipID9.C04.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996176 2015-04-15 2015-05-20 2015-11-06 GSM1658187 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658187/suppl/GSM1658187_nochipID9.C09.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996177 2015-04-15 2015-05-20 2015-11-06 GSM1658188 SRA 1 Brain Homo sapiens cortex microglia postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658188/suppl/GSM1658188_nochipID9.C14.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996178 2015-04-15 2015-05-20 2015-11-06 GSM1658189 SRA 1 Brain Homo sapiens cortex microglia postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658189/suppl/GSM1658189_nochipID9.C18.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996179 2015-04-15 2015-05-20 2015-11-06 GSM1658190 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658190/suppl/GSM1658190_nochipID9.C26.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996180 2015-04-15 2015-05-20 2015-11-06 GSM1658191 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658191/suppl/GSM1658191_nochipID9.C37.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996181 2015-04-15 2015-05-20 2015-11-06 GSM1658192 SRA 1 Brain Homo sapiens cortex neurons postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658192/suppl/GSM1658192_nochipID9.C42.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996182 2015-04-15 2015-05-20 2015-11-06 GSM1658193 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658193/suppl/GSM1658193_nochipID9.C57.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996183 2015-04-15 2015-05-20 2015-11-06 GSM1658194 SRA 1 Brain Homo sapiens cortex neurons postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658194/suppl/GSM1658194_nochipID9.C59.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996184 2015-04-15 2015-05-20 2015-11-06 GSM1658195 SRA 1 Brain Homo sapiens cortex neurons postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658195/suppl/GSM1658195_nochipID9.C62.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996185 2015-04-15 2015-05-20 2015-11-06 GSM1658196 SRA 1 Brain Homo sapiens cortex microglia postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658196/suppl/GSM1658196_nochipID9.C65.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996186 2015-04-15 2015-05-20 2015-11-06 GSM1658197 SRA 1 Brain Homo sapiens cortex neurons postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658197/suppl/GSM1658197_nochipID9.C74.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996187 2015-04-15 2015-05-20 2015-11-06 GSM1658198 SRA 1 Brain Homo sapiens cortex neurons postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658198/suppl/GSM1658198_nochipID9.C75.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996188 2015-04-15 2015-05-20 2015-11-06 GSM1658199 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658199/suppl/GSM1658199_nochipID9.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996189 2015-04-15 2015-05-20 2015-11-06 GSM1658200 SRA 1 Brain Homo sapiens cortex neurons postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658200/suppl/GSM1658200_nochipID9.C85.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996190 2015-04-15 2015-05-20 2015-11-06 GSM1658201 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658201/suppl/GSM1658201_nochipID9.C87.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996191 2015-04-15 2015-05-20 2015-11-06 GSM1658202 SRA 1 Brain Homo sapiens cortex astrocytes postnatal 47 years nochipID9 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658202/suppl/GSM1658202_nochipID9.C92.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996192 2015-04-15 2015-05-20 2015-11-06 GSM1658203 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658203/suppl/GSM1658203_nochipID10.C02.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996193 2015-04-15 2015-05-20 2015-11-06 GSM1658204 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658204/suppl/GSM1658204_nochipID10.C03.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996194 2015-04-15 2015-05-20 2015-11-06 GSM1658205 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658205/suppl/GSM1658205_nochipID10.C05.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996195 2015-04-15 2015-05-20 2015-11-06 GSM1658206 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658206/suppl/GSM1658206_nochipID10.C07.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996196 2015-04-15 2015-05-20 2015-11-06 GSM1658207 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658207/suppl/GSM1658207_nochipID10.C11.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996197 2015-04-15 2015-05-20 2015-11-06 GSM1658208 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658208/suppl/GSM1658208_nochipID10.C16.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996198 2015-04-15 2015-05-20 2015-11-06 GSM1658209 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658209/suppl/GSM1658209_nochipID10.C17.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996199 2015-04-15 2015-05-20 2015-11-06 GSM1658210 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658210/suppl/GSM1658210_nochipID10.C19.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996200 2015-04-15 2015-05-20 2015-11-06 GSM1658211 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658211/suppl/GSM1658211_nochipID10.C25.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996201 2015-04-15 2015-05-20 2015-11-06 GSM1658212 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658212/suppl/GSM1658212_nochipID10.C26.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996202 2015-04-15 2015-05-20 2015-11-06 GSM1658213 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658213/suppl/GSM1658213_nochipID10.C37.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996203 2015-04-15 2015-05-20 2015-11-06 GSM1658214 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658214/suppl/GSM1658214_nochipID10.C39.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996204 2015-04-15 2015-05-20 2015-11-06 GSM1658215 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658215/suppl/GSM1658215_nochipID10.C42.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996205 2015-04-15 2015-05-20 2015-11-06 GSM1658216 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658216/suppl/GSM1658216_nochipID10.C44.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996206 2015-04-15 2015-05-20 2015-11-06 GSM1658217 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658217/suppl/GSM1658217_nochipID10.C47.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996207 2015-04-15 2015-05-20 2015-11-06 GSM1658218 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658218/suppl/GSM1658218_nochipID10.C49.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996208 2015-04-15 2015-05-20 2015-11-06 GSM1658219 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658219/suppl/GSM1658219_nochipID10.C50.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996209 2015-04-15 2015-05-20 2015-11-06 GSM1658220 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658220/suppl/GSM1658220_nochipID10.C53.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996210 2015-04-15 2015-05-20 2015-11-06 GSM1658221 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658221/suppl/GSM1658221_nochipID10.C58.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996211 2015-04-15 2015-05-20 2015-11-06 GSM1658222 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658222/suppl/GSM1658222_nochipID10.C65.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996212 2015-04-15 2015-05-20 2015-11-06 GSM1658223 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658223/suppl/GSM1658223_nochipID10.C74.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996213 2015-04-15 2015-05-20 2015-11-06 GSM1658224 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658224/suppl/GSM1658224_nochipID10.C75.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996214 2015-04-15 2015-05-20 2015-11-06 GSM1658225 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658225/suppl/GSM1658225_nochipID10.C85.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996215 2015-04-15 2015-05-20 2015-11-06 GSM1658226 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658226/suppl/GSM1658226_nochipID10.C88.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996216 2015-04-15 2015-05-20 2015-11-06 GSM1658227 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658227/suppl/GSM1658227_nochipID10.C93.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996217 2015-04-15 2015-05-20 2015-11-06 GSM1658228 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID10 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658228/suppl/GSM1658228_nochipID10.C94.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996218 2015-04-15 2015-05-20 2015-11-06 GSM1658229 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658229/suppl/GSM1658229_nochipID11.C02.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996219 2015-04-15 2015-05-20 2015-11-06 GSM1658230 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658230/suppl/GSM1658230_nochipID11.C03.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996220 2015-04-15 2015-05-20 2015-11-06 GSM1658231 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658231/suppl/GSM1658231_nochipID11.C06.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996221 2015-04-15 2015-05-20 2015-11-06 GSM1658232 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658232/suppl/GSM1658232_nochipID11.C07.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996222 2015-04-15 2015-05-20 2015-11-06 GSM1658233 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658233/suppl/GSM1658233_nochipID11.C08.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996223 2015-04-15 2015-05-20 2015-11-06 GSM1658234 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658234/suppl/GSM1658234_nochipID11.C10.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996224 2015-04-15 2015-05-20 2015-11-06 GSM1658235 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658235/suppl/GSM1658235_nochipID11.C15.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996225 2015-04-15 2015-05-20 2015-11-06 GSM1658236 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658236/suppl/GSM1658236_nochipID11.C17.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996226 2015-04-15 2015-05-20 2015-11-06 GSM1658237 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658237/suppl/GSM1658237_nochipID11.C19.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996227 2015-04-15 2015-05-20 2015-11-06 GSM1658238 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658238/suppl/GSM1658238_nochipID11.C20.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996228 2015-04-15 2015-05-20 2015-11-06 GSM1658239 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658239/suppl/GSM1658239_nochipID11.C21.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996229 2015-04-15 2015-05-20 2015-11-06 GSM1658240 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658240/suppl/GSM1658240_nochipID11.C22.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996230 2015-04-15 2015-05-20 2015-11-06 GSM1658241 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658241/suppl/GSM1658241_nochipID11.C23.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996231 2015-04-15 2015-05-20 2015-11-06 GSM1658242 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658242/suppl/GSM1658242_nochipID11.C25.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996232 2015-04-15 2015-05-20 2015-11-06 GSM1658243 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658243/suppl/GSM1658243_nochipID11.C30.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996233 2015-04-15 2015-05-20 2015-11-06 GSM1658244 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658244/suppl/GSM1658244_nochipID11.C37.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996234 2015-04-15 2015-05-20 2015-11-06 GSM1658245 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658245/suppl/GSM1658245_nochipID11.C48.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996235 2015-04-15 2015-05-20 2015-11-06 GSM1658246 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658246/suppl/GSM1658246_nochipID11.C49.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996236 2015-04-15 2015-05-20 2015-11-06 GSM1658247 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658247/suppl/GSM1658247_nochipID11.C50.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996237 2015-04-15 2015-05-20 2015-11-06 GSM1658248 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658248/suppl/GSM1658248_nochipID11.C53.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996238 2015-04-15 2015-05-20 2015-11-06 GSM1658249 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658249/suppl/GSM1658249_nochipID11.C54.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996239 2015-04-15 2015-05-20 2015-11-06 GSM1658251 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658251/suppl/GSM1658251_nochipID11.C55.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996240 2015-04-15 2015-05-20 2015-11-06 GSM1658253 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658253/suppl/GSM1658253_nochipID11.C56.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996241 2015-04-15 2015-05-20 2015-11-06 GSM1658255 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658255/suppl/GSM1658255_nochipID11.C57.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996242 2015-04-15 2015-05-20 2015-11-06 GSM1658257 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658257/suppl/GSM1658257_nochipID11.C58.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996243 2015-04-15 2015-05-20 2015-11-06 GSM1658259 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658259/suppl/GSM1658259_nochipID11.C59.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996244 2015-04-15 2015-05-20 2015-11-06 GSM1658262 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658262/suppl/GSM1658262_nochipID11.C60.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996245 2015-04-15 2015-05-20 2015-11-06 GSM1658264 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658264/suppl/GSM1658264_nochipID11.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996246 2015-04-15 2015-05-20 2015-11-06 GSM1658266 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658266/suppl/GSM1658266_nochipID11.C62.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996247 2015-04-15 2015-05-20 2015-11-06 GSM1658268 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658268/suppl/GSM1658268_nochipID11.C63.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996248 2015-04-15 2015-05-20 2015-11-06 GSM1658270 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658270/suppl/GSM1658270_nochipID11.C64.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996249 2015-04-15 2015-05-20 2015-11-06 GSM1658272 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658272/suppl/GSM1658272_nochipID11.C66.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996250 2015-04-15 2015-05-20 2015-11-06 GSM1658275 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658275/suppl/GSM1658275_nochipID11.C68.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996251 2015-04-15 2015-05-20 2015-11-06 GSM1658277 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658277/suppl/GSM1658277_nochipID11.C69.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996252 2015-04-15 2015-05-20 2015-11-06 GSM1658279 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658279/suppl/GSM1658279_nochipID11.C75.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996253 2015-04-15 2015-05-20 2015-11-06 GSM1658281 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658281/suppl/GSM1658281_nochipID11.C76.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996254 2015-04-15 2015-05-20 2015-11-06 GSM1658284 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658284/suppl/GSM1658284_nochipID11.C77.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996255 2015-04-15 2015-05-20 2015-11-06 GSM1658286 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658286/suppl/GSM1658286_nochipID11.C78.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996256 2015-04-15 2015-05-20 2015-11-06 GSM1658288 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658288/suppl/GSM1658288_nochipID11.C79.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996257 2015-04-15 2015-05-20 2015-11-06 GSM1658290 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658290/suppl/GSM1658290_nochipID11.C81.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996258 2015-04-15 2015-05-20 2015-11-06 GSM1658292 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658292/suppl/GSM1658292_nochipID11.C82.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996259 2015-04-15 2015-05-20 2015-11-06 GSM1658294 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658294/suppl/GSM1658294_nochipID11.C83.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996260 2015-04-15 2015-05-20 2015-11-06 GSM1658297 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658297/suppl/GSM1658297_nochipID11.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996261 2015-04-15 2015-05-20 2015-11-06 GSM1658299 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658299/suppl/GSM1658299_nochipID11.C86.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996262 2015-04-15 2015-05-20 2015-11-06 GSM1658301 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658301/suppl/GSM1658301_nochipID11.C91.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996263 2015-04-15 2015-05-20 2015-11-06 GSM1658304 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID11 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658304/suppl/GSM1658304_nochipID11.C93.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996264 2015-04-15 2015-05-20 2015-11-06 GSM1658305 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658305/suppl/GSM1658305_nochipID13.C07.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996265 2015-04-15 2015-05-20 2015-11-06 GSM1658306 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658306/suppl/GSM1658306_nochipID13.C11.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996266 2015-04-15 2015-05-20 2015-11-06 GSM1658307 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658307/suppl/GSM1658307_nochipID13.C12.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996267 2015-04-15 2015-05-20 2015-11-06 GSM1658308 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658308/suppl/GSM1658308_nochipID13.C14.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996268 2015-04-15 2015-05-20 2015-11-06 GSM1658309 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658309/suppl/GSM1658309_nochipID13.C15.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996269 2015-04-15 2015-05-20 2015-11-06 GSM1658310 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658310/suppl/GSM1658310_nochipID13.C17.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996270 2015-04-15 2015-05-20 2015-11-06 GSM1658311 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658311/suppl/GSM1658311_nochipID13.C21.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996271 2015-04-15 2015-05-20 2015-11-06 GSM1658312 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658312/suppl/GSM1658312_nochipID13.C25.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996272 2015-04-15 2015-05-20 2015-11-06 GSM1658313 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658313/suppl/GSM1658313_nochipID13.C28.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996273 2015-04-15 2015-05-20 2015-11-06 GSM1658314 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658314/suppl/GSM1658314_nochipID13.C32.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996274 2015-04-15 2015-05-20 2015-11-06 GSM1658315 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658315/suppl/GSM1658315_nochipID13.C36.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996275 2015-04-15 2015-05-20 2015-11-06 GSM1658316 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658316/suppl/GSM1658316_nochipID13.C45.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996276 2015-04-15 2015-05-20 2015-11-06 GSM1658317 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658317/suppl/GSM1658317_nochipID13.C46.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996277 2015-04-15 2015-05-20 2015-11-06 GSM1658318 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658318/suppl/GSM1658318_nochipID13.C48.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996278 2015-04-15 2015-05-20 2015-11-06 GSM1658319 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658319/suppl/GSM1658319_nochipID13.C50.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996279 2015-04-15 2015-05-20 2015-11-06 GSM1658320 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658320/suppl/GSM1658320_nochipID13.C55.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996280 2015-04-15 2015-05-20 2015-11-06 GSM1658321 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658321/suppl/GSM1658321_nochipID13.C57.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996281 2015-04-15 2015-05-20 2015-11-06 GSM1658322 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658322/suppl/GSM1658322_nochipID13.C58.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996282 2015-04-15 2015-05-20 2015-11-06 GSM1658323 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658323/suppl/GSM1658323_nochipID13.C59.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996283 2015-04-15 2015-05-20 2015-11-06 GSM1658324 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658324/suppl/GSM1658324_nochipID13.C61.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996284 2015-04-15 2015-05-20 2015-11-06 GSM1658325 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658325/suppl/GSM1658325_nochipID13.C63.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996285 2015-04-15 2015-05-20 2015-11-06 GSM1658326 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658326/suppl/GSM1658326_nochipID13.C64.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996286 2015-04-15 2015-05-20 2015-11-06 GSM1658327 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658327/suppl/GSM1658327_nochipID13.C66.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996287 2015-04-15 2015-05-20 2015-11-06 GSM1658328 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658328/suppl/GSM1658328_nochipID13.C67.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996288 2015-04-15 2015-05-20 2015-11-06 GSM1658329 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658329/suppl/GSM1658329_nochipID13.C68.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996289 2015-04-15 2015-05-20 2015-11-06 GSM1658330 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658330/suppl/GSM1658330_nochipID13.C72.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996290 2015-04-15 2015-05-20 2015-11-06 GSM1658331 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658331/suppl/GSM1658331_nochipID13.C73.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996291 2015-04-15 2015-05-20 2015-11-06 GSM1658332 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658332/suppl/GSM1658332_nochipID13.C74.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996292 2015-04-15 2015-05-20 2015-11-06 GSM1658333 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658333/suppl/GSM1658333_nochipID13.C75.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996293 2015-04-15 2015-05-20 2015-11-06 GSM1658334 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658334/suppl/GSM1658334_nochipID13.C80.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996294 2015-04-15 2015-05-20 2015-11-06 GSM1658335 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658335/suppl/GSM1658335_nochipID13.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996295 2015-04-15 2015-05-20 2015-11-06 GSM1658336 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658336/suppl/GSM1658336_nochipID13.C87.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996296 2015-04-15 2015-05-20 2015-11-06 GSM1658337 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID13 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina MiSeq ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658337/suppl/GSM1658337_nochipID13.C93.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996297 2015-04-15 2015-05-20 2015-11-06 GSM1658338 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658338/suppl/GSM1658338_nochipID4.C03.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996298 2015-04-15 2015-05-20 2015-11-06 GSM1658339 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658339/suppl/GSM1658339_nochipID4.C04.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996299 2015-04-15 2015-05-20 2015-11-06 GSM1658340 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658340/suppl/GSM1658340_nochipID4.C10.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996300 2015-04-15 2015-05-20 2015-11-06 GSM1658341 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658341/suppl/GSM1658341_nochipID4.C14.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996301 2015-04-15 2015-05-20 2015-11-06 GSM1658342 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658342/suppl/GSM1658342_nochipID4.C18.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996302 2015-04-15 2015-05-20 2015-11-06 GSM1658343 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658343/suppl/GSM1658343_nochipID4.C19.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996303 2015-04-15 2015-05-20 2015-11-06 GSM1658344 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658344/suppl/GSM1658344_nochipID4.C20.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996304 2015-04-15 2015-05-20 2015-11-06 GSM1658345 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658345/suppl/GSM1658345_nochipID4.C21.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996305 2015-04-15 2015-05-20 2015-11-06 GSM1658346 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658346/suppl/GSM1658346_nochipID4.C33.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996306 2015-04-15 2015-05-20 2015-11-06 GSM1658347 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658347/suppl/GSM1658347_nochipID4.C34.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996307 2015-04-15 2015-05-20 2015-11-06 GSM1658348 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658348/suppl/GSM1658348_nochipID4.C38.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996308 2015-04-15 2015-05-20 2015-11-06 GSM1658349 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658349/suppl/GSM1658349_nochipID4.C39.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996309 2015-04-15 2015-05-20 2015-11-06 GSM1658350 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658350/suppl/GSM1658350_nochipID4.C41.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996310 2015-04-15 2015-05-20 2015-11-06 GSM1658351 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658351/suppl/GSM1658351_nochipID4.C42.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996311 2015-04-15 2015-05-20 2015-11-06 GSM1658352 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658352/suppl/GSM1658352_nochipID4.C44.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996312 2015-04-15 2015-05-20 2015-11-06 GSM1658353 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658353/suppl/GSM1658353_nochipID4.C49.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996313 2015-04-15 2015-05-20 2015-11-06 GSM1658354 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658354/suppl/GSM1658354_nochipID4.C52.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996314 2015-04-15 2015-05-20 2015-11-06 GSM1658355 SRA 1 Brain Homo sapiens cortex fetal_replicating prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658355/suppl/GSM1658355_nochipID4.C53.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996315 2015-04-15 2015-05-20 2015-11-06 GSM1658356 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658356/suppl/GSM1658356_nochipID4.C59.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996316 2015-04-15 2015-05-20 2015-11-06 GSM1658357 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658357/suppl/GSM1658357_nochipID4.C62.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996317 2015-04-15 2015-05-20 2015-11-06 GSM1658358 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658358/suppl/GSM1658358_nochipID4.C63.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996318 2015-04-15 2015-05-20 2015-11-06 GSM1658359 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658359/suppl/GSM1658359_nochipID4.C66.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996319 2015-04-15 2015-05-20 2015-11-06 GSM1658360 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658360/suppl/GSM1658360_nochipID4.C74.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996320 2015-04-15 2015-05-20 2015-11-06 GSM1658361 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658361/suppl/GSM1658361_nochipID4.C77.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996321 2015-04-15 2015-05-20 2015-11-06 GSM1658362 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658362/suppl/GSM1658362_nochipID4.C78.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996322 2015-04-15 2015-05-20 2015-11-06 GSM1658363 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658363/suppl/GSM1658363_nochipID4.C84.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996323 2015-04-15 2015-05-20 2015-11-06 GSM1658364 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658364/suppl/GSM1658364_nochipID4.C89.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996324 2015-04-15 2015-05-20 2015-11-06 GSM1658365 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658365/suppl/GSM1658365_nochipID4.C95.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996325 2015-04-15 2015-05-20 2015-11-06 GSM1658366 SRA 1 Brain Homo sapiens cortex fetal_quiescent prenatal 16-18 W nochipID4 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. Single cell from healthy human cortex Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1). Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ). Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no). Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample RNA-Seq transcriptomic cDNA Illumina NextSeq 500 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1658nnn/GSM1658366/suppl/GSM1658366_nochipID4.C96.csv.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX996/SRX996326 2015-04-14 2015-05-20 2017-10-06 GSE67835 26060301

We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained from epileptic patients during temporal lobectomy for medically refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain.

Examination of cell types in healthy human brain samples. Expression profiling by high throughput sequencing ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP057/SRP057196 ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67835/suppl/GSE67835_RAW.tar