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Sample GSM850476 Query DataSets for GSM850476
Status Public on Feb 01, 2012
Title OS25 cells mRNA-Seq
Sample type SRA
Source name Undifferentiated ES cells
Organism Mus musculus
Characteristics cell line: OS25 ES cells
Growth protocol Mouse ES-OS25 cells were grown on 0.1% gelatin-coated surfaces in GMEM-BHK21 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 1% MEM non-essential amino acids, 1 mM sodium pyruvate (all from Gibco), 50 μM 2-mercaptoethanol, 1000 U/ml of human recombinant leukaemia inhibitory factor (Chemicon) and 0.1 mg/ml Hygromycin (Roche).
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from ES-OS25 cells by TRIzol extraction using Phase Lock Gel tubes and 8 µg prepared for mRNA sequencing. Quality of total RNA was assessed by bioanalyser before library preparation. The mRNA-seq library was prepared according to Illumina’s instructions (#1004898 Rev A) with some modifications. After selection of polyA-containing mRNA molecules, RNA was further depleted for ribosomal RNA (rRNA) using the Ribominus kit (Invitrogen). The library was quantified by Qubit, and library size was assessed by Bioanalyzer before high-throughput sequencing.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using RNA implementation of CASAVA 1.6 software allowing 2 mismatches and unique reads only. Multiple sequencing runs per sample were merged and used to create wiggle and bigwig(bw) summary files.
Submission date Dec 17, 2011
Last update date May 15, 2019
Contact name Ines de Santiago
Phone +44 (0) 2083838526
Organization name MRC Clinical Sciences Centre
Department Epigenetics
Lab Genome Function
Street address Hammersmith Hospital Campus
City London
ZIP/Postal code W12 0NN
Country United Kingdom
Platform ID GPL11002
Series (2)
GSE34519 mRNA-seq and expression profile of mouse ES OS25 cells
GSE34520 Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ES cells
SRA SRX112175
BioSample SAMN00766448
Named Annotation

Supplementary file Size Download File type/resource 715.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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