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Dataset View [GSE67835]

Series	GSE67835
Title	A survey of human brain transcriptome diversity at the single cell level
Year	2015
Country	Sweden
Article	Quake 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
PMID	26060301
Bio Project	BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA281204
Sra	SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP057196
Overall Desgin	Examination of cell types in healthy human brain samples.
Summary	We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained from epileptic patients during temporal lobectomy for medically refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain.
Experimental Protocol	C1 autoprep standard protocol; C1 autoprep standard protocol, followed by clontech single 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 processing	Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy -lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1).; Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif ).; Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty -s no).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample
Platform	GPL15520;GPL18573
Public On	Public on May 20 2015

Cell Groups

Differential Expression Gene List

cortex astrocytes_VS_cortex endothelial cortex astrocytes_VS_cortex fetal-quiescent cortex astrocytes_VS_cortex fetal-replicating cortex astrocytes_VS_cortex hybrid cortex astrocytes_VS_cortex microglia cortex astrocytes_VS_cortex neurons cortex astrocytes_VS_cortex oligodendrocytes cortex astrocytes_VS_cortex OPC cortex astrocytes_VS_hippocampus endothelial cortex astrocytes_VS_hippocampus hybrid cortex astrocytes_VS_hippocampus microglia cortex astrocytes_VS_hippocampus neurons cortex astrocytes_VS_hippocampus oligodendrocytes cortex astrocytes_VS_hippocampus OPC cortex endothelial_VS_cortex fetal-quiescent cortex endothelial_VS_cortex fetal-replicating cortex endothelial_VS_cortex hybrid cortex endothelial_VS_cortex microglia cortex endothelial_VS_cortex neurons cortex endothelial_VS_cortex oligodendrocytes cortex endothelial_VS_cortex OPC cortex endothelial_VS_hippocampus endothelial cortex endothelial_VS_hippocampus hybrid cortex endothelial_VS_hippocampus microglia cortex endothelial_VS_hippocampus neurons cortex endothelial_VS_hippocampus oligodendrocytes cortex endothelial_VS_hippocampus OPC cortex fetal-quiescent_VS_cortex fetal-replicating cortex fetal-quiescent_VS_cortex hybrid cortex fetal-quiescent_VS_cortex microglia cortex fetal-quiescent_VS_cortex neurons cortex fetal-quiescent_VS_cortex oligodendrocytes cortex fetal-quiescent_VS_cortex OPC cortex fetal-quiescent_VS_hippocampus endothelial cortex fetal-quiescent_VS_hippocampus hybrid cortex fetal-quiescent_VS_hippocampus microglia cortex fetal-quiescent_VS_hippocampus neurons cortex fetal-quiescent_VS_hippocampus oligodendrocytes cortex fetal-quiescent_VS_hippocampus OPC cortex fetal-replicating_VS_cortex hybrid cortex fetal-replicating_VS_cortex microglia cortex fetal-replicating_VS_cortex neurons cortex fetal-replicating_VS_cortex oligodendrocytes cortex fetal-replicating_VS_cortex OPC cortex fetal-replicating_VS_hippocampus endothelial cortex fetal-replicating_VS_hippocampus hybrid cortex fetal-replicating_VS_hippocampus microglia cortex fetal-replicating_VS_hippocampus neurons cortex fetal-replicating_VS_hippocampus oligodendrocytes cortex fetal-replicating_VS_hippocampus OPC cortex hybrid_VS_cortex microglia cortex hybrid_VS_cortex neurons cortex hybrid_VS_cortex oligodendrocytes cortex hybrid_VS_cortex OPC cortex hybrid_VS_hippocampus endothelial cortex hybrid_VS_hippocampus hybrid cortex hybrid_VS_hippocampus microglia cortex hybrid_VS_hippocampus neurons cortex hybrid_VS_hippocampus oligodendrocytes cortex hybrid_VS_hippocampus OPC cortex microglia_VS_cortex neurons cortex microglia_VS_cortex oligodendrocytes cortex microglia_VS_cortex OPC cortex microglia_VS_hippocampus endothelial cortex microglia_VS_hippocampus hybrid cortex microglia_VS_hippocampus microglia cortex microglia_VS_hippocampus neurons cortex microglia_VS_hippocampus oligodendrocytes cortex microglia_VS_hippocampus OPC cortex neurons_VS_cortex oligodendrocytes cortex neurons_VS_cortex OPC cortex neurons_VS_hippocampus endothelial cortex neurons_VS_hippocampus hybrid cortex neurons_VS_hippocampus microglia cortex neurons_VS_hippocampus neurons cortex neurons_VS_hippocampus oligodendrocytes cortex neurons_VS_hippocampus OPC cortex oligodendrocytes_VS_cortex OPC cortex oligodendrocytes_VS_hippocampus endothelial cortex oligodendrocytes_VS_hippocampus hybrid cortex oligodendrocytes_VS_hippocampus microglia cortex oligodendrocytes_VS_hippocampus neurons cortex oligodendrocytes_VS_hippocampus oligodendrocytes cortex oligodendrocytes_VS_hippocampus OPC cortex OPC_VS_hippocampus endothelial cortex OPC_VS_hippocampus hybrid cortex OPC_VS_hippocampus microglia cortex OPC_VS_hippocampus neurons cortex OPC_VS_hippocampus oligodendrocytes cortex OPC_VS_hippocampus OPC hippocampus endothelial_VS_hippocampus hybrid hippocampus endothelial_VS_hippocampus microglia hippocampus endothelial_VS_hippocampus neurons hippocampus endothelial_VS_hippocampus oligodendrocytes hippocampus endothelial_VS_hippocampus OPC hippocampus hybrid_VS_hippocampus microglia hippocampus hybrid_VS_hippocampus neurons hippocampus hybrid_VS_hippocampus oligodendrocytes hippocampus hybrid_VS_hippocampus OPC hippocampus microglia_VS_hippocampus neurons hippocampus microglia_VS_hippocampus oligodendrocytes hippocampus microglia_VS_hippocampus OPC hippocampus neurons_VS_hippocampus oligodendrocytes hippocampus neurons_VS_hippocampus OPC hippocampus oligodendrocytes_VS_hippocampus OPC

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