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Series GSE255089 Query DataSets for GSE255089
Status Public on Jun 03, 2024
Title Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells (chip-seq gradient)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report an in-depth 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 Examination of histone and transcription factor enrichment by MNase ChIP-seq at canonical nucleosomes and subnucleosomal particles in mouse embryonic stem cells.
 
Contributor(s) Nocente M, Mesihovic Karamitsos A, Drouineau E, Chantalat S, Gérard M
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Submission date Feb 05, 2024
Last update date Jun 04, 2024
Contact name Matthieu Gerard
E-mail(s) gerard.team.cea@gmail.com
Organization name CEA
Lab LEM
Street address Route Nationale
City Gif-sur-yvette
ZIP/Postal code 91191
Country France
 
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (42)
GSM8063832 Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Smarcb1-depleted auxin 20h replicate 1
GSM8063833 Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Smarcb1-depleted auxin 20h replicate 2
GSM8063834 Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Arid1a-depleted auxin 20h replicate 1
Relations
BioProject PRJNA1073502

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Supplementary file Size Download File type/resource
GSE255089_RAW.tar 7.2 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA

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