|
| 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 |
mRNA_ESC_OS25.bw; 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 |
| E-mail(s) |
desantiago.ines07@imperial.ac.uk
|
| 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 |
|
| Relations |
| SRA |
SRX112175 |
| BioSample |
SAMN00766448 |
| Named Annotation |
GSM850476_mRNA_ESC_OS25.bw |
