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Series GSE64825 Query DataSets for GSE64825
Status Public on Jan 26, 2016
Title Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary This study describes the distribution and functional analysis of ATP-dependent chromatin remodelers in mouse 46C ES cells. The remodelers for which ChIP-Seq profiles were generated are Brg1, Chd1, Chd2, Chd4, Chd6, Chd8, Chd9 and Ep400. We first generated ES cell lines expressing individual remodelers fused to an affinity tag at the C-terminus, from their endogenous loci. Remodelers were then formaldehyde-crosslinked to chromatin in vivo, MNase digested to release individual nucleosomes, then immunoprecipitated sequentially with two distinct antibodies against the tag. DNA fragments immunoprecipitated with each factor were then identified by high throughput sequencing. Control experiments were realized by applying the same protocol to untagged ES cells. Pol II distribution was examined by ChIP-exo in ES cells depleted of either Ep400, Brg1 and Chd4. Chromatin access was studied by ATAC-seq in remodeler-depleted cells. Finally, nucleosomal occupancy was explored by MNase-seq.
Overall design ChIP-Seq profiling, FAIRE-seq profiling, RNA-Seq profiling, ATAC-seq profiling, MNase-seq profiling, ChIP-exo profiling on mouse ES cells
Contributor(s) Hmitou I, de Dieuleveult M, Depaux A, Chantalat S, Yen K, Pugh BF, Gérard M
Citation(s) 26814966
Submission date Jan 09, 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
Platforms (5)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (44)
GSM1581286 Smarca4 ChIP-Seq replicate 1
GSM1581287 Smarca4 ChIP-Seq replicate 2
GSM1581288 Chd1 ChIP-Seq replicate 1
BioProject PRJNA272126
SRA SRP051966

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Supplementary file Size Download File type/resource
GSE64825_RAW.tar 9.1 Gb (http)(custom) TAR (of BEDGRAPH, BW, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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