|
| Status |
Public on Dec 04, 2012 |
| Title |
mRNA-seq: ES KAP1 KO (ES3 cells) |
| Sample type |
SRA |
| |
|
| Source name |
mRNA-seq: ES KAP1 KO (ES3 cells)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Embryonic stem cells (ES3)
time-point: KO: 4 days post 4-OHT inducible CRE
|
| Growth protocol |
ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma: G5154) with sodium pyruvate (used at 1mM, Sigma: S8636), MEM non-essential amino acids (used at 1x, Gibco: 11140-035), L-glutamine (used at 2mM, Gibco: 25030-024), 2-mercaptoethanol (used at 0.1mM, Sigma), ES cell tested FBS (Gibco: 16141-079) and leukaemia inhibitory factor (LIF, used at 1,000 units/ml, Chemicon: ESG1107). Cells were grown on 0.2% gelatin (Sigma: 48723-500G-F)-coated plates and split every two days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After pooling duplicates, total RNA was extracted with TRizol (Invitrogen: 15596-018), purified using a PureLink RNA kit (Ambion: 12183018A) and treated with DNase (Ambion: AM1907) before checking the quality on a bioanalyzer and using 10ug for mRNA-seq library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
See also Rowe et al., 2010 for analysis of this data for ERV expression
|
| Data processing |
Raw reads were mapped to the mouse genome and transcriptome using Bowtie
Peaks were called using MACS
For histone modifications, enriched regions were defined using the ChIP-part suite
Genome_build: mm9
|
| |
|
| Submission date |
Nov 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Adamandia Kapopoulou |
| E-mail(s) |
adamandia.kapopoulou@epfl.ch
|
| Phone |
0041216930940
|
| Organization name |
EPFL
|
| Department |
Sciences de la Vie
|
| Lab |
Trono
|
| Street address |
Station 15
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE41903 |
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells |
|
| Relations |
| SRA |
SRX202982 |
| BioSample |
SAMN01801722 |
