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Sample GSM1941472 Query DataSets for GSM1941472
Status Public on Jan 26, 2016
Title Chd4 knockdown pol II ChIP-exo replicate 2
Sample type SRA
 
Source name Chd4 knockdown pol II ChIP-exo, ESC
Organism Mus musculus
Characteristics strain: 46C (129/Ola strain)
cell line: ESC line 46C
transfection: shRNA vector targeting Chd4, replicate 2
chip antibody: Pol II Antibody (N-20) (Santa Cruz Biotechnology, catalog# sc-899, lot# A2014)
Treatment protocol described in the SAMPLES section (experimental conditions)
Growth protocol Embryonic stem cells were cultured at 37°C, 5% CO2, on mitomycin C-inactivated mouse embryonic fibroblasts, in DMEM (Sigma) with 15% foetal bovine serum and leukemia inhibitory factor (LIF).
Extracted molecule genomic DNA
Extraction protocol ChIP-exo using an antibody anti-RNA polymerase II: The immunoprecipitation step was performed using antibodies against Pol II (sc-899, Santa Cruz Biotechnology) attached to magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and lambda and recJ exonuclease digestion on the beads.
After elution, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina adaptor was then ligated, and the products PCR-amplified and gel-purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description library strategy: ChIP-exo
Data processing Basecalls was performed using Bcl2FastQ version 2.16.0. Sequenced reads were masked for low-quality sequence, then mapped to mm9 whole genome using bwa mem 0.7.9a with the default parameters
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using WigMaker 3 with default parameters; Scores represent the maximum number of reads overlapping in a 25 bp bin
Supplementary_files_format_and_content: BIGWIG files were generated with UCSC tools (v4) using WigToBigWig program
 
Submission date Nov 16, 2015
Last update date May 15, 2019
Contact name Matthieu GERARD
E-mail(s) matthieu.gerard@cea.fr
Organization name CEA
Department I2BC
Lab Mammalian Epigenomics
Street address SBIGeM bldg 142
City Gif-sur-Yvette
ZIP/Postal code 91191
Country France
 
Platform ID GPL19057
Series (1)
GSE64825 Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cells
Relations
BioSample SAMN04271229
SRA SRX1433582

Supplementary file Size Download File type/resource
GSM1941472_Pol2_ChIP-exo_Chd4-knockdown_replicate_2_57910mm9.wig.gz 56.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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