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Dataset View [GSE73727]

SeriesGSE73727
TitleSingle-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
Year2016
CountryAustria
ArticleKubicek S,Bock C,Berishvili E,Barbieux C,Spittler A,Penz T,Farlik M,Klughammer J,Li J.Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.EMBO reports.2016 Feb
PMID26691212
Bio ProjectBioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA297774
SraSRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP064464
Overall DesginTranscriptional dissection of human pancreatic islets of one donor using single-cell RNA-seq
SummaryWe report the single-cell RNA-seq based identification of 6 known human islet cell types (alpha cells, beta cells, delta cells, pp cells, acinar cells and duct cells) based on the expression of known marker genes. We further assess cell type specific gene expression and suggest novel marker genes for several cell types.
Experimental ProtocolTo disassociate islets into single cells, islets were incubated in Accutase (Life technology) in 37 °C for 20 min, neutralized by CMRL medium. Purification of single cells was performed by flow cytometry cell sorting on a Moflo AstriosEQ (Beckman Coulter, Miami); cDNA synthesis and enrichment was performed following the Smart-seq2 protocol as described (Picelli et al., 2014).
Data processingTrimming of adapter sequences was performed with trimmomatic (v 0.32) minimum read length after trimming: 25; Alignment of the trimmed reads to the human transcriptome (hg19 GRCh37 ftp://ftp.ensembl.org/pub/release-74/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.74.cdna.all.fa.gz) was performed with bowtie1 (v 1.1); Calculation of normalized transcript-wise expression estimates (RPKM values) was performed based on the transcriptome alignments using the R (v 3.1.2) package BitSeq (v 1.10.0). Function: getExpression() with uniform=FALSE; Genome_build: hg19; Supplementary_files_format_and_content: Tab-delimited text files include transcript-wise RPKM values or read counts for each sample
PlatformGPL11154
Public OnPublic on Jan 05 2016

Cell Groups

Differential Expression Gene List

KEGG GO Others   

Gene SymbolEnsembl IDFDR
ENSG000002271640.000655331762188376
FCRL3ENSG000001608560.000675657094049368
DYNC1I1ENSG000001585600.000676252721989786
SEPT6ENSG000001253540.000677665438541363
ENSG000002608810.000677705799373805
ENSG000002233530.000699281193908391
TMEM173ENSG000001845840.000708238224176633
CCNJENSG000001074430.000709654323786581
KLRC3ENSG000002058100.000709654323786581
SPARCL1ENSG000001525830.000709837365555019
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