GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL10773 GPL11002

23 Samples

Download data: BED, CEL, TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: TXT

(Submitter supplied) 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:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10773

12 Samples

Download data: CEL

(Submitter supplied) 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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

11 Samples

Download data: BED, TXT

(Submitter supplied) Cell differentiation requires epigenetic modulation of tissue-specific genes and activities of master transcriptional regulators, which are recognized for their dominant control over cellular programs. Using novel epigenomic methods, we characterized enhancer elements specifically modified in differentiating intestinal epithelial cells and found enrichment of transcription factor-binding motifs corresponding to CDX2, a master regulator of the intestine. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL9115 GPL10773

17 Samples

Download data: BED, BW, CEL, TXT

(Submitter supplied) Transcriptional profiling of undifferentiated HIEC cells stably infected with a retroviral inducible expression vector (RevTet system) comparing DOX-induced HIEC pTetON with DOX-induced HIEC cells expressing either HNF1 and CDX2 or HNF1, CDX2 plus GATA4. Keywords: Differential gene expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6854

8 Samples

Download data: TAV

(Submitter supplied) To define target genes of the intestine-restricted transcription factor (TF) CDX2 in intestinal stem cells, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq). We used RNA-sequencing to profile gene expression changes during cell differentiation from mouse intestinal stem cells to mature villus cells, as well as genes perturbed in intestinal stem cells upon loss of Cdx2. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

11 Samples

Download data: BED, BW, GTF, TXT

(Submitter supplied) Intestinal differentiation during endoderm development We used RNA-sequencing to profile gene expression changes during the embryonic development of the gastrointestinal tract.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

74 Samples

Download data: TXT

(Submitter supplied) Important lineage regulators, such as the intestinal lineage regulator CDX2, can function over the timespan of intestinal development. The consequences of CDX2 knockout in the embryo versus in the adult are quite distinct. The data below provide a rationale for these divergent transcription factor functions in distinct developmental contexts, with unique binding patterns of CDX2 observed via ChIP-seq and unique gene regulatory targets defined via RNA-seq. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21626 GPL21697

21 Samples

Download data: BW, TXT

(Submitter supplied) Gene expression was compared between E18.5 Gata4Gata6 double conditional knockout (cKO) small intestinal epithelium and E18.5 control mouse small intestinal epithleium.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

6 Samples

Download data: CEL

(Submitter supplied) HNF4 paralogs are redundantly required for proper villus elongation, differentiation and maturation in the developing gut. We find 5,391 chromatin regions become inaccessible upon HNF4 loss, and HNF4 binding sequences are most enriched in these regions. Genes nearby these 5,391 HNF4 dependent regions are associated with villus differentiation/maturation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

3 Samples

Download data: BED, BW

(Submitter supplied) Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where constitutive signaling causes cancer. Genome-wide analysis of DNA cis-regulatory regions bound by the intestine-restricted transcription factor CDX2 in colonic cells uncovered highly significant over-representation of sequences that bind TCF4, a transcriptional effector of intestinal Wnt signaling. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

8 related Platforms

56 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL11044

13 Samples

Download data: BED, CEL, TXT, XLS

(Submitter supplied) Epigenetic analysis on mouse gastric organoids overexpressing either CDX2, HNF4A or control GFP. Epigenetic analyses include ATAC-seq, Cut&Run. Mouse gastric and intestinal stem cell ATAC-seq and mouse gastric antrum and intestinal villus ChIP-seq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23969 GPL21273

44 Samples

Download data: BW, CSV

(Submitter supplied) Background and Aims: Hepatocyte nuclear factor 1 (HNF1) transcription factors direct tissue specific gene regulation in liver, pancreas and kidney and are associated with diabetes. Here we investigate the transcriptional network governed by HNF1 in an intestinal epithelial cell line. Methods: Chromatin immunoprecipitation followed by direct sequencing (ChIP-seq) was used to identify HNF1 binding sites genome-wide. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: BED

(Submitter supplied) We determined changes in enhancer chromatin that occur during colonic inflammation, found that dynamic chromatin regions are enriched for HNF4A binding motirfs, and then measured HNF4A binidng by ChIP-seq in each condition.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT, WIG

(Submitter supplied) GATA6 is a transcription factor involved in the differentiation of intestinal epithelial cells into differentiated absorptive epithelial cells. GATA6 is expressed in all segments of the small intestine. We examined the impact of deleting GATA6 from intestinal epithelial cells of the adult ileum

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

6 Samples

Download data: CEL

(Submitter supplied) Understanding the enhancer activity in MTA2 regulates colonic intestine epithelial fate and tissue plasticity.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

5 Samples

Download data: BED, BW

(Submitter supplied) To test the hypothesis that HNF4A should engage small intestine enhancers in colon and activate transcription, we over-expressed HNF4A in 2 independent mouse colonic orgnaoid lines and 5 independent human colonic organoid lines and performed RNA-seq studies. Both RNA-seq data revealed that small intestine functional pathways including fat, protein and carbohydrate digestion and absorption were activated after HNF4A OE. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

14 Samples

Download data: CSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL24247

40 Samples

Download data: BED, BW