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Series GSE14586 Query DataSets for GSE14586
Status Public on Oct 01, 2009
Title Cdx2 Binding Sites On Cdx2 Expressing ES Cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary A) Chromatins were prepared from Cdx2-inducible ES cells cultured for 48 - 60 hours in the Dox+ and Dox- conditions. Chromatin immunoprecipitation (ChIP) was carried out by using anti-FLAG M2 affinity gel. ChIP product was tested by Western blotting using anti-FLAG antibody. Nuclear extract from ES cells cultured for 48 - 60 hours in Dox+ and Dox- condition was used for the Western blot.
B) CDX2 ChIP-Seq peaks in the Hoxa7 gene region. UCSC Mouse Mm9 browser view of Hoxa7 gene locus after mapping CDX2 ChIP-Seq tags locations in the wiggle format. CDX2 ChIP-Seq peaks are shown in red color.
C) Cdx2 ChIP-Seq result was verified by qPCR. Target genes were indicated in (G). Primers flanking a promoter region of Hbb-b1 and Pou5f1 as well as a gene desert region in chromosome 3 were used as negative controls. Primers flanking of Actb gene promoter were used for normalization. The relative enrichment of CDX2 binding was indicated as fold change.
(D) CDX2-binding motifs identified with CisFinder using 200 bp sequences centered at ChIP sites.
(F) Potential CDX2-direct target genes based on ChIP-Seq and the alteration of expression by Cdx2-overexpression.
(G) Identification of CDX2 target genes by combining information on binding sites with gene expression response to Cdx2 over-expression
Overall design Chromatin IP against CDX2-Flag fusion protein. MC1 ES cells were genetically modified for ROSA26 locus to have Tet-Off expression cassette for C-terminal FLAG tagged Cdx2.
The peaks are obtained from the Eland Multi Alignment file.
The number of tags in peaks was compared with the number of tags in the control sample for the same region corrected by the total coverage of tags.
See supplemental file of the paper for details.
Contributor(s) Sharov AA, Thomas MP, Islam MN, Longo DL, Ko MS
Citation(s) 19796622
Submission date Jan 27, 2009
Last update date May 15, 2019
Contact name Minoru S.H. Ko
Phone 410-558-8359
Organization name NIH
Department National Institute on Aging
Lab Lab of Genetics
Street address 251 Bayview Blvd, Suite 100, 10C
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (2)
GSM364858 Cdx2_ChIPSeq
GSM701423 control
This SubSeries is part of SuperSeries:
GSE16375 Uncovering early response of gene regulatory networks in ES cells by systematic induction of transcription factors
SRA SRP001367
BioProject PRJNA123173

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
GSE14586_RAW.tar 1.0 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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