Loading

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
RPRD1AENSG000001414250.00831186775153241
NDUFS4ENSG000001642580.00832227731263125
TRAM1ENSG000000671670.00833301137805749
IFT88ENSG000000327420.00838473492329755
ADAM32ENSG000001971400.00839912403469146
ENSG000002324600.00839912403469146
VPS29ENSG000001112370.00841336691185808
FXYD6ENSG000001377260.00842936515293227
UTYENSG000001838780.00843539286364295
NCOR1P1ENSG000002401080.00843539286364295
Displaying 1141-1150 of 1218 results.