GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1901506 Query DataSets for GSM1901506
Status Public on Jan 05, 2016
Title islet_single_cell_52
Sample type SRA
Source name pancreatic islet
Organism Homo sapiens
Characteristics assigned cell type: beta
qc pass: TRUE
cell count: 1
ercc_mix: mix2
ercc_dilution: 1000000
Treatment protocol Islets were cultured in CMRL medium (Life technology) supplemented with 10% FBS, 2 mM glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin.
Extracted molecule polyA RNA
Extraction 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).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
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 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
Submission date Oct 05, 2015
Last update date May 15, 2019
Contact name Christoph Bock
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
Platform ID GPL11154
Series (1)
GSE73727 Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
BioSample SAMN04145807
SRA SRX1304194

Supplementary file Size Download File type/resource
GSM1901506_sample_52_RPKM.tsv.gz 4.2 Mb (ftp)(http) TSV
GSM1901506_sample_52_counts.tsv.gz 2.0 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap