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Sample GSM594578 Query DataSets for GSM594578
Status Public on Oct 31, 2010
Title ChIP-Seq for H3K27ac in ES (129JAE-C57/B6) cells 1
Sample type SRA
 
Source name Embyonic stem cells
Organism Mus musculus
Characteristics chip antibody: H3K27ac
antibody catalog number: Abcam AB4729
cell type: embryonic stem cells
Growth protocol V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 200 and 350bp (representing shear fragments between 100 and 250nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Chromatin IP against H3K27ac
Data processing Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using MAQ (phred score 50).
For all samples aligned sequences were extended 600bp upstream and 400bp downstream (with respect to read strand) for transcription histone marks and and 200bp upstream and 0bp downstream (with respect to read strand) for transcription factors, allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
 
Submission date Sep 16, 2010
Last update date May 15, 2019
Contact name Menno P Creyghton
E-mail m.creyghton@hubrecht.eu
Organization name Hubrecht Institute
Lab Creyghton
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
 
Platform ID GPL9250
Series (2)
GSE24164 ChIP-Seq of chromatin marks at distal enhancers in Mouse Embryonic Stem Cells and adult tissues.
GSE24165 Histone H3K27ac separates active from poised enhancers and predicts developmental state
Relations
SRA SRX027331
BioSample SAMN00113682
Named Annotation GSM594578_MC2_ES_H3K27ac_wig_min0.5.WIG.gz

Supplementary file Size Download File type/resource
GSM594578_MC2_ES_H3K27ac1.q50.m1.txt.gz 26.6 Mb (ftp)(http) TXT
GSM594578_MC2_ES_H3K27ac_wig_min0.5.WIG.gz 43.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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