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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 04, 2012 |
| Title |
mRNA-seq: ES KAP1 WT (Rex1GFP ES cells) |
| Sample type |
SRA |
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| Source name |
mRNA-seq: ES KAP1 WT (Rex1GFP ES cells)
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| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
cell type: Embryonic stem cells (Rex1GFP, Wray et al., Nat Cell Biol. 2011)
time-point: 4 days post puromycin selection of empty shRNA vector
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Nov 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Adamandia Kapopoulou |
| E-mail(s) |
adamandia.kapopoulou@epfl.ch
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| Phone |
0041216930940
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| Organization name |
EPFL
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| Department |
Sciences de la Vie
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| Lab |
Trono
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| Street address |
Station 15
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE41903 |
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells |
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| Relations |
| SRA |
SRX202985 |
| BioSample |
SAMN01801725 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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