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Sample GSM1438698 Query DataSets for GSM1438698
Status Public on Sep 16, 2015
Title pol2_KO_ChIPSeq
Sample type SRA
 
Source name MEFs cells knockout MED23
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblast
genotype/variation: MED23 knockout
chip antibody: Pol II
Growth protocol MEFs cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (vol/vol) FBS (Hyclone)
Extracted molecule genomic DNA
Extraction protocol Cell lysates were sonicated and immunoprecipitated DNA-protein complex using antibody (Millipore, Cat. #05-1312, Lot #DAM1567819); Pol II (N20, Santa Cruz, Cat. sc-899).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing CASAVA version 1.6 used for base-calling
Sequencing reads were alligned to mouse genome by Bowtie version 0.12. 8 and parameters are followings:-v1, --best, --strata, -k2, -m1
Peak calling was performed independently for each sample using MACS software version 1.4.2 by p-value threshold of 1e-5
Genome_build: mm9
Supplementary_files_format_and_content: wiggle files were generated using MACS version 1.4.2. Scores represent fragments pileup at every 10 bps of ChIP-seq.
 
Submission date Jul 17, 2014
Last update date May 15, 2019
Contact name Gang Wang
Organization name Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Department Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology,
Lab Gang Wang's Lab
Street address Yueyang Road 320
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL11002
Series (1)
GSE59518 The Mediator complex subunit MED23 couples H2B mono-ubiquitination to transcriptional control and cell fate determination
Relations
BioSample SAMN02921331
SRA SRX655689

Supplementary file Size Download File type/resource
GSM1438698_pol2_KO_ChIPSeq.wig.gz 105.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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