Dataset View [GSE67835]

TitleA survey of human brain transcriptome diversity at the single cell level
ArticleQuake SR,Barres BA,Hayden Gephart MG,Shuer LM,Caneda C,Enge M,Zhang Y,Sloan SA,Darmanis S.A survey of human brain transcriptome diversity at the single cell level.Proceedings of the National Academy of Sciences of the United States of America.2015 Jun 9
Bio ProjectBioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA281204
SraSRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP057196
Overall DesginExamination of cell types in healthy human brain samples.
SummaryWe 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.
Experimental ProtocolC1 autoprep standard protocol; C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol; Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system.
Data processingShort read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy -lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1).; Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif ).; Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty -s no).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample
Public OnPublic on May 20 2015

Cell Groups

Differential Expression Gene List

KEGG GO Others   

Gene SymbolEnsembl IDFDR
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