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Series GSE210444 Query DataSets for GSE210444
Status Public on Jun 13, 2023
Title Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report a comprehensive analysis of nucleosomal and subnucleosomal organization at cis-regulatory elements (CREs) in mouse embryonic stem (ES) cells. We used chromatin fragmented by a moderate dose of micrococcal nuclease (MNase) as input for ChIP-seq with antibodies against histones and transcription factors and high-coverage deep-sequencing. Centrifugation of chromatin through sucrose gradients, followed by ChIP-seq, allowed the characterization of different subclasses of subnucleosomal particles having distribution patterns specific to enhancers, gene promoters and CTCF binding sites. We also provide datasets showing that this particular chromatin organization of CREs is conserved in the human melanoma 501Mel cell line.
Overall design We used MNase ChIP-seq to define the distribution of subnucleosomal particles, canonical nucleosomes, and transcription factors enrichment.
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Contributor(s) Nocente MC, Mesihovic Karamitsos A, Drouineau E, Chantalat S, Gérard M
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Submission date Aug 03, 2022
Last update date Jun 14, 2023
Contact name Matthieu Gerard
Organization name CEA
Street address Route Nationale
City Gif-sur-yvette
ZIP/Postal code 91191
Country France
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (85)
GSM6430364 Histone H3 MNase ChIP-seq top of gradient (3-4) replicate 1
GSM6430365 Histone H3 MNase ChIP-seq top of gradient (3-4) replicate 2
GSM6430366 Histone H3 MNase ChIP-seq top of gradient (2-3-4) replicate 1
BioProject PRJNA865739

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Supplementary file Size Download File type/resource
GSE210444_RAW.tar 19.5 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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