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Series GSE40910 Query DataSets for GSE40910
Status Public on Oct 21, 2012
Title Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We determined genome-wide nucleosome occupancy in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell type and protein specific binding preferences of transcription factors to sites with either low (e.g. Myc, Klf4, Zfx) or high (e.g. Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome depleted regions around transcription start and termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to their CpG-content or histone methylation marks. Throughout the genome nucleosome occupancy was dependent on the presence of certain histone methylation or acetylation modifications. In addition, the average nucleosome-repeat length increased during differentiation by 5-7 base pairs, with local variations for specific genomic regions. Our results reveal regulatory mechanisms of cell differentiation acting through nucleosome repositioning.
Overall design We have determined genome-wide nucleosome position maps in mouse embryonic stem cells (ESCs), neural progenitor cells (NPCs) derived from these ESCs by retinoic acid induced differentiation as well as mouse embryonic fibroblasts (MEFs) from the corresponding mouse strain
Contributor(s) Teif VB, Rippe K
Citation(s) 23085715
Submission date Sep 14, 2012
Last update date May 15, 2019
Contact name Vladimir B Teif
Organization name University of Essex
Department School of Life Sciences
Street address Wivenhoe Park
City Colchester
ZIP/Postal code CO4 3SQ
Country United Kingdom
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (3)
GSM1004652 NPC merged mononucleosomes
GSM1004653 ESC merged mononucleosomes
GSM1004654 MEF merged mononucleosomes
This SubSeries is part of SuperSeries:
GSE40896 Genome-wide nucleosome positioning during embryonic stem cell development
SRA SRP015795
BioProject PRJNA175501

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Supplementary file Size Download File type/resource
GSE40910_RAW.tar 9.0 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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