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Dataset View [GSE73727]

Series	GSE73727
Title	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
Year	2016
Country	Austria
Article	Kubicek 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
PMID	26691212
Bio Project	BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA297774
Sra	SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP064464
Overall Desgin	Transcriptional dissection of human pancreatic islets of one donor using single-cell RNA-seq
Summary	We 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 Protocol	To 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 processing	Trimming 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
Platform	GPL11154
Public On	Public on Jan 05 2016

Cell Groups

Differential Expression Gene List

pancreatic islet_VS_pancreatic islet acinar pancreatic islet_VS_pancreatic islet alpha pancreatic islet_VS_pancreatic islet beta pancreatic islet_VS_pancreatic islet delta pancreatic islet_VS_pancreatic islet duct pancreatic islet_VS_pancreatic islet pp pancreatic islet acinar_VS_pancreatic islet alpha pancreatic islet acinar_VS_pancreatic islet beta pancreatic islet acinar_VS_pancreatic islet delta pancreatic islet acinar_VS_pancreatic islet duct pancreatic islet acinar_VS_pancreatic islet pp pancreatic islet alpha_VS_pancreatic islet beta pancreatic islet alpha_VS_pancreatic islet delta pancreatic islet alpha_VS_pancreatic islet duct pancreatic islet alpha_VS_pancreatic islet pp pancreatic islet beta_VS_pancreatic islet delta pancreatic islet beta_VS_pancreatic islet duct pancreatic islet beta_VS_pancreatic islet pp pancreatic islet delta_VS_pancreatic islet duct pancreatic islet delta_VS_pancreatic islet pp pancreatic islet duct_VS_pancreatic islet pp

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