Loading

Dataset View [GSE67835]

SeriesGSE67835
TitleA survey of human brain transcriptome diversity at the single cell level
Year2015
CountrySweden
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
PMID26060301
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
PlatformGPL15520;GPL18573
Public OnPublic on May 20 2015

Cell Groups

Differential Expression Gene List

KEGG GO Others   

Gene SymbolEnsembl IDFDR
GLI3ENSG000001065710.00331655187593971
MON2ENSG000000619870.00331655187593971
NCOR1ENSG000001410270.00340817317925681
NDRG2ENSG000001657950.00370793147427225
SIRPAENSG000001980530.00380707414278385
LOC1004994660.00383140981404387
ACBD7ENSG000001762440.00426140843506938
PDLIM5ENSG000001631100.00438341734959228
COX7A2ENSG000001126950.00451611103104096
PSMD1ENSG000001736920.00481797042974601
Displaying 161-170 of 199 results.