NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1901469 Query DataSets for GSM1901469
Status Public on Jan 05, 2016
Title islet_single_cell_15
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 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
 
Submission date Oct 05, 2015
Last update date May 15, 2019
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
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
Relations
BioSample SAMN04145842
SRA SRX1304157

Supplementary file Size Download File type/resource
GSM1901469_sample_15_RPKM.tsv.gz 4.2 Mb (ftp)(http) TSV
GSM1901469_sample_15_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