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Series GSE35599 Query DataSets for GSE35599
Status Public on Jun 15, 2012
Title Relocalization of retinoic acid receptors from non-canonical to canonical spaced binding elements during embryoid body differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Retinoic Acid Receptors (RARs) bind RA-response elements in regulatory regions of their target genes. While canonical RAREs comprise direct repeats of the consensus 5’-RGKTCA-3’ sequence separated by 1, 2 or 5 nucleotides (DR1, DR2, DR5), we show that shortly after RA treatement of mouse embryoid bodies or F9 cells, RARs occupy a large repertoire of DR0, DR2, DR5, DR8 and IR0 elements. In vitro, RAR-RXR bind these non-canonical spacings with comparable affinities to DR2 and DR5. Most DR8 elements comprise three half sites with DR2 and DR0 spacings. This specific half site organisation constitutes a previously unrecognised, but frequent signature of RAR binding elements and acts as an RARE. At later stages of embryoid body differentiation, RARs relocalise to a restricted repertoire of sites comprising predominantly DR5 elements. Differentiation thus involves genomic relocalisation of RARs, and a switch from DR0 and DR8 at early times to DR5 at later stages.
Overall design Examination of genomic localisation of RAR in differentiating embryoid bodies.
Contributor(s) Moutier E, Ye T, Choukrallah M, Urban S, Osz J, Chatagnon A, Delacroix L, Langer D, Rochel N, Moras D, Benoit G, Davidson I
Citation(s) 22661711
Submission date Feb 07, 2012
Last update date May 15, 2019
Contact name Tao YE
Organization name IGBMC (CNRS/INSERM/UDS)
Street address 1 rue Laurent Fries
City Illkirch
ZIP/Postal code 67404
Country France
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM871395 RA 2h ChIPSeq
GSM871396 RA 24h ChIPSeq
GSM871397 RA 24h RNASeq
SRA SRP010781
BioProject PRJNA152519

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Supplementary file Size Download File type/resource
GSE35599_RAW.tar 611.7 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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