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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
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
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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