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Series GSE37889 Query DataSets for GSE37889
Status Public on Dec 30, 2015
Title PLURIPOTENCY REGULATOR ZIC3 IS AN EARLY LINEAGE SPECIFIER
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Sustained expression of the key pluripotency transcriptional regulators and proliferative factors is needed for the maintenance of embryonic stem cells and early progenitors of various lineages. Zic3 is one of those factors which has been shown to be important for embryonic stem cell pluripotency. Through combinatorial analysis of transcription factor binding sites and the corresponding gene-regulation, we show that Zic3 not only activates key pluripotency genes but also acts cooperatively with them in connecting important circuits of regulation in ES cell in proliferation and maintenance of early progenitors.
 
Overall design Chromatin immunoprecipitation was performed as previously described (Loh, Y.H. et al, Nat Genet 38, 431-440 (2006)). Briefly, cells were treated with 1% formaldehyde for 10 mins at RT. The reaction was quenched with 125 mM glycine. Chromatin was harvested from nuclear extracts. Chromatin extracts were sonicated to an average size of 500 bp. Immunoprecipitation was performed using 10 µg of Zic3 antibody previously generated (Lim, L.S. et al., Mol Biol Cell 18, 1348-1358 (2007)). Immunoprecipitated chromatin extracts were subjected to sequencing.
 
Contributor(s) HONG FH, Kumar V, STANTON LW
Citation(s) 20872845
Submission date May 09, 2012
Last update date May 15, 2019
Contact name Vibhor Kumar
E-mail(s) kumarv1@gis.a-star.edu.sg
Organization name Genome Institute of Singapore
Department CMB-6
Street address 60 Biopolis Street, Genome, #02-01
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (2)
GSM929462 ChIPseq-mES-Zic3
GSM929463 ChIPseq-mES-Input
Relations
BioProject PRJNA165125
SRA SRP013000

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Supplementary file Size Download File type/resource
GSE37889_RAW.tar 187.4 Mb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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