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Sample GSM1032187 Query DataSets for GSM1032187
Status Public on Dec 04, 2012
Title mRNA-seq: ES KAP1 KD (Rex1GFP ES cells)
Sample type SRA
Source name mRNA-seq: ES KAP1 KD (Rex1GFP ES cells)
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 KAP1 shRNA vector
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 HiSeq 2000
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
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 GPL13112
Series (1)
GSE41903 TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
SRA SRX202986
BioSample SAMN01801726

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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