NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE38371 Query DataSets for GSE38371
Status Public on Jan 17, 2013
Title Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (RNA-seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary According to current models, transcription factors (TFs) activated by extracellular stimuli operate in the context of a pre-established enhancer repertoire induced and maintained by lineage-specific TFs. Here, we uncovered the existence of latent enhancers, defined as regions of the genome that in terminally differentiated cells are poorly accessible and lack the histone marks characteristic of enhancers, but readily acquire these features in response to extracellular cues. Stimulation of resting macrophages caused simultaneous binding of stimulus-activated TFs and lineage-determining TFs to these regions, enabling deposition of enhancer-specific features. Once unveiled, these enhancers did not return to a latent state even when stimulation ceased; instead, they persisted and mediated a faster and stronger response upon restimulation. We suggest that stimulus-specific expansion of the available cis-regulatory repertoire provides an epigenomic memory of the exposure to environmental agents.
 
Overall design Poly(A) fraction of the total mRNA of resting and stimulated murine bone marrow derived macrophages was extracted and subjected to by multiparallel sequencing. Experiments carried out in untreated cells as well as in cells treated for 4hrs (IFNg, IL4, TNFa, TGFb1, IL1b, MALP2, CpG)
 
Contributor(s) Ostuni R, Piccolo V, Barozzi I, Polletti S, Ghisletti S, Natoli G
Citation(s) 23332752
Submission date May 31, 2012
Last update date Sep 21, 2020
Contact name Iros Barozzi
E-mail(s) iros.barozzi@meduniwien.ac.at
Organization name Medical University Vienna
Street address Borschkegasse 8a
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (8)
GSM940701 BMDM cells No treatment
GSM940702 BMDM cells IFNg
GSM940703 BMDM cells IL4
This SubSeries is part of SuperSeries:
GSE38379 Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire
Relations
BioProject PRJNA167769
SRA SRP013465

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
GSE38371_RAW.tar 15.7 Mb (http)(custom) TAR (of TXT)
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
External link. Please review our privacy policy.