GEO DataSets

(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) To investigate whether the H3K27ac is involved in the development of inflammatory bowal disease. We established dextran sulfate sodium (DSS)-induced chronic colitis and performed RNA-sequencing and Chromatin Immunoprecipitation followed by NGS sequencing for H3K27ac in the mice colon tissues. We find that the global H3K27ac distribution in colon tissue had no significant difference, while on the typical-enhancers specific in the DSS group, H3K27ac signals were significantly enriched when compared with the control. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BW

(Submitter supplied) The transcriptional regulation of drug-metabolizing enzymes and transporters (here collectively referred to as DMEs) in the developing proximal tubule is not well understood. As in the liver, DME regulation in the PT may be mediated through nuclear receptors which are thought to “sense” deviations from homeostasis by being activated by ligands, some of which are handled by DMEs, including drug transporters. more...

Organism:

Rattus norvegicus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14844

8 Samples

Download data: TXT

(Submitter supplied) Background & Aims: HNF4α is an important transcriptional regulator of hepatocyte and pancreatic function. Hnf4α deletion is embryonically lethal with severe defects in visceral endoderm formation, liver maturation and colon development. However, the precise role of this transcription factor in maintaining homeostasis of the adult intestine remains unclear. Herein, we aimed to elucidate the adult intestinal functions of Hnf4α. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5284

Platform:

GPL1261

6 Samples

Download data: CEL

Analysis of hepatocyte nuclear factor 4 alpha (HNF4-alpha) deficient colons of 1 year old animals. HNF4-alpha is a transcription factor. Deletion of HNF4-alpha confined to the epithelial colon. Results provide insight into the role of HNF4-alpha in maintaining intestinal inflammatory homeostasis.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE11759

6 Samples

Download data: CEL

(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) 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) To gain a deeper understanding of the genetic basis of liver repopulation after injury, we utilize an innovative technique to profile the expression changes and chromatin landscape during the regenerative response. We utilize the Fah-/- mouse, a model for hereditary tyrosinemia deficient in fumarylacetoacetate hydrolase (FAH), that undergoes repopulation with FAH-expressing hepatocytes. We employ translating ribosome affinity purification followed by RNA-sequencing (TRAP-seq) and assay for transposase accessible chromatin using sequencing (ATAC-seq) to specifically isolate regenerating hepatocytes and performed high-throughput sequencing to identify the dynamic genomic and epigenomic changes during liver repopulation.

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL21103

26 Samples

Download data: BIGWIG, XLS

(Submitter supplied) Here we employed the genetically engineered mice models (GEM) to uncover the role of gut epithelial EZH2 in the pathogenesis of colitis. To dissect the underlying mechanism, Chip-Seq analysis is used for mechanistic study. From the result we find EZH2 mainly targeted in the TSS region. As we have known TNF-alpha pathway can be regulated by EZH2, we try and find TRAF2/5 may be the key point for EZH2 to regulated TNF-alpha pathway. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: BW

(Submitter supplied) Despite recent progress, the contribution of epigenetic mechanisms to govern Inflammatory bowel disease (IBD) pathogenesis remains elusive. Here we show that epithelial EZH2, the catalytic subunit of PRC2 is critical for experimental colitis. Depletion of EZH2 in intestinal epithelial cells sensitized the cells to DSS-induced colitis in mice. To dissect underlying mechanism, we conducted gene expression profile analysis (RNA-Seq) by using primary Intestinal epithelial cells (IECs) isolated from EZH2 WT and KO mice to gain molecular insights into the affected biological processes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: TXT

(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:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

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

(Submitter supplied) RNA-sequening colonic epithelium with deeper reads to evaluate consequence of mta2 gene loss in the colonic epithelium.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: TXT

(Submitter supplied) CRISPR knock out the NuRD and SWI/SNF complex gene from mouse colonic organoids to validate the potential function with SATB2.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: TXT

(Submitter supplied) We use ChIP-seq to understand the genomic binding sites of MTA2 in colonic epithelium and to study the shifting of SATB2 and HNF4A's genomic binding sites after MTA2 loss in colonic epithelium.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

10 Samples

Download data: BED, BW

(Submitter supplied) Background: Genome wide association studies (GWASs) have revealed many susceptibility loci for complex genetic diseases. For most loci the causal genes have not been identified. The identification of candidate genes is currently mainly based genes that localize close to or within the identified loci. We have recently shown that 92 of the 163 Inflammatory Bowel Disease (IBD)-loci co-localize with noncoding DNA regulatory elements (DRE). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

372 Samples

Download data: WIG

(Submitter supplied) Hepatocyte-nuclear-factor-4α (Hnf4α) is a transcription factor that controls epithelial cell polarity and maturation during embryogenesis. Hnf4α conditional deletion during post-natal development results in minor consequences on intestinal epithelium integrity but promotes activation of the Wnt/β-catenin pathway. Here we show that Hnf4α does not act as a tumor suppressor gene but is crucial to promote gut tumorigenesis in mice. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) To further understand different gene expression of miR-31 knockout mouse colon and normal colon, we have employed colonic epithelium microarray expression profiling as a discovery platform to identify different genes with miR-31 knockout mouse colon and normal colon.comparision with normal colonic epithelium,upgene is 285 and downgene is 178 in knockout group.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

6 Samples

Download data: TXT