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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 04, 2012 |
| Title |
H3K27ac ChIP: KAP1 WT TI |
| Sample type |
SRA |
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| Source name |
H3K27ac ChIP: KAP1 WT TI
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Embryonic stem cells (ES3)
time-point: 4 days post puromycin selection of empty shRNA vector
chip antibody: None (Total Input)
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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 |
genomic DNA |
| Extraction protocol |
ES cell samples were washed 2x (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x24mm tubes (Covaris: 520056) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 30 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine). Samples were also checked for the absence of single-stranded DNA by Exonuclease I treatment.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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 |
SRX202991 |
| BioSample |
SAMN01801731 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data not provided for this record |
| Raw data are available in SRA |
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