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Sample GSM1581296 Query DataSets for GSM1581296
Status Public on Jan 26, 2016
Title Chd8 ChIP-Seq replicate 1
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics strain: 46C (129/Ola strain)
cell line: TAP-tag introduced by homologous recombination at the gene encoding Chd8
chip antibodies: sequential ChIP whith HA and FLAG antibodies
Treatment protocol none
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 Formaldehyde-fixed chromatin was digested by MNase to release individual nucleosomes
Libraries were prepared according to the Illumina ChIP-seq protocol. Following end-repair and adapter ligation, fragments were size-selected on an agarose gel to purify genomic DNA fragments between 140 and 180 bp. Purified fragments were next amplified before clustering and single-read sequencing
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina Genome Analyzer IIx
 
Data processing Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity/low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7 with parameters -a -m1 --best --strata -v2 p3
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
 
Submission date Jan 09, 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 GPL11002
Series (1)
GSE64825 Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cells
Relations
BioSample SAMN03280132
SRA SRX835508

Supplementary file Size Download File type/resource
GSM1581296_wigs_for_Chd8_SAC100_rep1.wig.gz 152.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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