| 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 |
|---|
