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The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (expression data)

ABSTRACT: We established whether partner transcription factor binding, chromatin structure, or gene expression is compromised upon loss of partner factors cdx2 or hnf4a in mouse intestinal villi This metadata file describes the gene expression componant of that data

ORGANISM(S): Mus musculus

PROVIDER: GSE34567 | GEO | 2013/02/05

SECONDARY ACCESSION(S): PRJNA156203

REPOSITORIES: GEO

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The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (ChIP-seq data)

2013-02-05 | GSE34566 | GEO

The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (ChIP-seq data)

Project description:We established whether partner transcription factor binding, chromatin structure, or gene expression is compromised upon loss of partner factors cdx2 or hnf4a in mouse intestinal villi. This metadata file describes the ChIP-seq componant of that data Intestinal epithelia were collected from mouse jejunum using EDTA-based chelation and ChIP-seq was performed, followed by next generation sequencing.

2013-02-05 | E-GEOD-34566 | biostudies-arrayexpress

The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (expression data)

Project description:We established whether partner transcription factor binding, chromatin structure, or gene expression is compromised upon loss of partner factors cdx2 or hnf4a in mouse intestinal villi This metadata file describes the gene expression componant of that data Intestinal epithelia were collected from mouse jejunum using EDTA-based chelation and RNA was made using trizol. RNA was checked for quality and then processed for affymetrix arrays, 430 2.0.

2013-02-05 | E-GEOD-34567 | biostudies-arrayexpress

Cdx2 transcription factor binding in intestinal villus and gene expression profiling in Cdx mutant mice

Project description:We conditionally inactivated mouse Cdx2, a dominant regulator of intestinal development, and mapped its genome occupancy in adult intestinal villi. Although homeotic transformation, observed in Cdx2-null embryos, was absent in mutant adults, gene expression and cell morphology were vitally compromised. Lethality was accelerated in mice lacking both Cdx2 and its homolog Cdx1, with exaggeration of defects in crypt cell replication and enterocyte differentiation. Cdx2 occupancy correlated with hundreds of transcripts that fell but not with equal numbers that rose with Cdx loss, indicating a predominantly activating role at intestinal cis-regulatory regions. Integrated consideration of a mutant phenotype and cistrome hence reveals the continued and distinct requirement in adults of a master developmental regulator that activates tissue-specific genes. Cdx2 ChIP-seq in mouse villus, and gene expression data from Cdx1, Cdx2 and compound knockout mouse intestine

2011-04-13 | E-GEOD-24633 | biostudies-arrayexpress

Cdx2 transcription factor binding in intestinal villus and gene expression profiling in Cdx mutant mice

2011-04-13 | GSE24633 | GEO

Cdx2 Binding Sites On Cdx2 Expressing ES Cells

Project description: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 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.

2009-10-01 | E-GEOD-14586 | biostudies-arrayexpress

Transcription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction With the Transcription Factor CDX2

Project description:To determine whether the intestine-restricted transcription factor (TF) CDX2 functionally interacts with the endoderm-wide TF HNF4A, we crossed tissue-specific conditional Cdx2 and Hnf4a knockout mice to generate compound mutant mice. We used RNA-sequencing to profile gene expression changes in compound mutant mice compared to control mice. The compound mutant mice had a significantly worse phenotype than either single mutant, and gene expression was significantly perturbed in compound mutants compared to control mice. Total RNA isolated from control and compound mutant (Hnf4a-del;Cdx2-del) jejunal mouse intestinal epithelium was prepared for sequencing using the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions. 75-base-pair single-end reads were sequenced on an Illumina NextSeq 500 instrument. The data include 2 independent biological replicates per genotype.

2014-12-08 | E-GEOD-62633 | biostudies-arrayexpress

Ectopic expression of the homeobox gene Cdx2 in the epiblast

Project description:This dataset describes the transcriptomic profiling by mRNA-seq of head tissues of E10.5 control or ectopically Cdx2-expressing embryos. Each condition was analyzed in 3 heads to address the role of Cdx2 in embryonic axis determination.

2019-11-04 | GSE123559 | GEO

Ectopic expression of the homeobox gene Cdx2 in hematopoietic stem cells

Project description:This dataset describes the transcriptomic profiling by mRNA-seq of the bone marrow of mice either wild type or ectopically expressing the homeobox gene Cdx2 in hematopoietic stem cells. Each condition was analyzed in triplicates to address the role of Cdx2 in leukemogenesis.

2021-07-05 | GSE120487 | GEO

Transcription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction With the Transcription Factor CDX2

2014-12-08 | GSE62633 | GEO

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