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Sample GSM1032198 Query DataSets for GSM1032198
Status Public on Dec 04, 2012
Title KAP1 ChIP: KAP1 WT IP
Sample type SRA
 
Source name KAP1 ChIP: KAP1 WT IP
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Embryonic stem cells (ES3)
time-point: WT cells cultured for 4 days
chip antibody: Tronolab, rabbit polyclonal SY 3267-68
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 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. Immunoprecipitations were performed in duplicates or triplicates with Dynabeads (100.03D) using 1-2x10e6 cells, 80ul pre-blocked beads and 5ug antibody (or no antibody as a control) per sample in IP buffer (167mM NaCl, 16.7mM Tris pH 8.1, 1.2mM EDTA, 0.5mM EGTA, 1.1%TritonX100 and protease inhibitors) overnight. After washing and reverse cross-linking (also overnight) and DNA extraction, results were quantified by SYBR green qPCR.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description The file "rbcc_wt_vs_ti_peaks.bed" was used in this paper: 586 of the 3099 peaks mapped here are included inĀ our other Kap1 ChIP-seq (GSM773067_kap1.bed) that was performed in E14 cells.
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 SRX202997
BioSample SAMN01801737

Supplementary file Size Download File type/resource
GSM1032198_rbcc_wt_vs_ko_peaks.bed.gz 34.3 Kb (ftp)(http) BED
GSM1032198_rbcc_wt_vs_ti_peaks.bed.gz 44.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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