GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE27841 Query DataSets for GSE27841
Status Public on Jan 03, 2012
Title Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation (ChIP-seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcription factors and chromatin modifiers play important roles in programming and reprogramming of cellular states during development. Much is known about the role of these regulators in gene activation, but relatively little is known about the critical process of enhancer silencing during differentiation. Here we show that the H3K4/K9 histone demethylase LSD1 plays an essential role in decommissioning enhancers during differentiation of embryonic stem cells (ESCs). LSD1 occupies enhancers of active genes critical for control of ESC state. However, LSD1 is not essential for maintenance of ESC identity. Instead, ESCs lacking LSD1 activity fail to fully differentiate and ESC-specific enhancers fail to undergo the histone demethylation events associated with differentiation. At enhancers, LSD1 is a component of the NuRD complex, which contains additional subunits that are necessary for ESC differentiation. We propose that the LSD1-NuRD complex decommissions enhancers of the pluripotency program upon differentiation, which is essential for complete shutdown of the ESC gene expression program and the transition to new cell states.
Overall design This is the ChIP-seq part of the study.

NOTE: We are unable to provide the sequencing data for the IgG control sample because it was never generated. The IgG control sample described in Figure 3c of Whyte et al., 2012 served as a control for the co-immunoprecipation and western blot experiments performed and shown in Figure 3. It was not used in sequencing experiments, and therefore was not sequenced and uploaded to GEO. Please inform those requesting this dataset of this fact.
Contributor(s) Whyte W, Bilodeau S, Hoke H, Orlando DA, Frampton GM, Young RA
Citation(s) 22297846
Submission date Mar 08, 2011
Last update date May 15, 2019
Contact name Richard A Young
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (24)
GSM687277 HDAC1 mES_ChipSeq
GSM687278 HDAC1 mES biological replicate
GSM687279 HDAC2 mES_ChipSeq
This SubSeries is part of SuperSeries:
GSE27844 Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation
SRA SRP005969
BioProject PRJNA141891

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE27841_RAW.tar 1.7 Gb (http)(custom) TAR (of WIG, YLF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap