GEO DataSets

(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) Cdx2/IL-1beta mice have less intestinal metaplasia at the squamocolumnar junction thanIL-1beta mice alone. This study was to identify a mechanism for this effect by examining differences in gene expression patterns when Cdx2 is co-expressed.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

6 Samples

Download data: CEL, XLSX

(Submitter supplied) Background & Aims: Tissue metaplasia is uncommon in adults because established cis-element programs resist rewiring. In Barrett’s esophagus, the distal esophageal mucosa acquires predominantly intestinal character, with notable gastric features, and is predisposed to develop invasive cancers. We sought to understand the chromatin underpinnings of Barrett’s metaplasia and why it commonly displays simultaneous gastric and intestinal properties. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL18573

40 Samples

Download data: BED, BW, MTX, TSV

(Submitter supplied) Understanding how silent genes can be competent for activation provides insight into development as well as cellular reprogramming and pathogenesis. We performed genomic location analysis of the pioneer transcription factor FoxA in the adult liver and found that about one-third of the FoxA bound sites are near silent genes, including genes without detectable RNA polymerase II. Virtually all of the FoxA-bound silent sites are within extended conserved sequences, suggesting possible function. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10774

3 Samples

Download data: 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) 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) We induced an intestinal metaplasia in human gastric mucosa in vitro, followed by the overexpression of CDX2 gene using a tet-on system.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: 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) 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: BW, CSV, NARROWPEAK

(Submitter supplied) It is not known why cancers arising in anatomically distinct locations but within the same tissue type can exhibit stark differences in molecular, pathological and clinical features. Cancers arising in proximal and distal sites of the colon are emblematic of these above differences as the proximal and distal colon cancers harbor differences in key molecular features, with BRAFV600E oncogene predominantly occurring in proximal colon cancers in the context of the increased promoter DNA methylation phenotype (CIMP-high), while distal colon cancers lack these molecular features. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: CSV

(Submitter supplied) It is not known why cancers arising in anatomically distinct locations but within the same tissue type can exhibit stark differences in molecular, pathological and clinical features. Cancers arising in proximal and distal sites of the colon are emblematic of these above differences as the proximal and distal colon cancers harbor differences in key molecular features, with BRAFV600E oncogene predominantly occurring in proximal colon cancers in the context of the increased promoter DNA methylation phenotype (CIMP-high), while distal colon cancers lack these molecular features. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we performed ATAC-seq of exogenously Sox4-expressed hepatocytes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: BW, XLS

(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:

GPL24247 GPL19057 GPL30172

72 Samples

Download data: BED, BW, XLS

(Submitter supplied) Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event. To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we exogenosly expressed Sox4 in adult hepatocytes, and profiled its binding sites in a genome wide manner by CUT&RUN-seq. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30172

24 Samples

Download data: BED, BW

(Submitter supplied) Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event. To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we exogenosly expressed Sox4 in adult hepatocytes, and profiled its binding sites in a genome wide manner by CUT&RUN-seq. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: BED, BW

(Submitter supplied) Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we performed ATAC-seq of exogenously Sox4-expressed hepatocytes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BW, XLS

(Submitter supplied) Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event. To investigate the effect of Sox4 on the transcriptomic changes in hepatocytes, we performed RNA-seq of Sox4-overexpressed (OE) hepatocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. Here, by RNA-seq, we dissect the transcriptomic changes involving the reprogramming process at different stages.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT