GEO DataSets

(Submitter supplied) Organoids are a valuable 3D model to study the differentiated functions of the human intestinal epithelium. They are a particularly powerful tool to measure epithelial transport processs in health and disease. Though biological assays such as organoid swelling and intraluminal pH measurements are well established, their underlying functional genomics are not well characterized. Here we combine genome-wide analysis of open chromatin by ATAC-seq with transcriptome mapping by RNA-seq to define the genomic signature of human intestinal organoids (HIOs). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

9 Samples

Download data

(Submitter supplied) Organoids are a valuable 3D model to study the differentiated functions of the human intestinal epithelium. They are a particularly powerful tool to measure epithelial transport processs in health and disease. Though biological assays such as organoid swelling and intraluminal pH measurements are well established, their underlying functional genomics are not well characterized. Here we combine genome-wide analysis of open chromatin by ATAC-seq with transcriptome mapping by RNA-seq to define the genomic signature of human intestinal organoids (HIOs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: TXT

(Submitter supplied) goal of this study was A) to compare global RNA-sequencing (RNA-seq) profiles data of organoid- derived colonic epithelial cells cultured and differentiated in i) conventional suspension organoids cultures (n=3), ii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and stretch (n=4), iii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and with stretch (n=4), iv) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and without stretch (n=4), v) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and stretch (n=6), vi) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and stretch (n=4), vii) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and with stretch (n=4), viii) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and without stretch (n=4), ix) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and stretch (n=3), and B) to identify differences in transcriptome profiles of organoid- derived colonic epithelial cells between following two conditions, unstimulated and basolaterally stimulated with IL-22 (10pM, 100pM or 1nM) Colon Intestine-Chips.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

48 Samples

Download data: CSV

(Submitter supplied) Efficient generation of human induced pluripotent stem cell (hiPSC)-derived human intestinal organoids (HIOs) would facilitate the development of in vitro models for a variety of diseases that affect the gastrointestinal tract, such as inflammatory bowel disease or Cystic Fibrosis. 

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: H5

(Submitter supplied) Lung and hindgut directed differentiations with multiple protocols and time points

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

28 Samples

Download data

(Submitter supplied) The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease. The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features. Among the most challenging models is the generation of human bronchial epithelium at air-liquid interface (HBE-ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: CSV

(Submitter supplied) The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease.  The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features.  Among the most challenging models is the generation of human bronchial epithelium at air-liquid interface (HBE-ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis.  Here we perform open chromatin mapping by ATAC-seq and transcriptomics by RNA-seq in parallel, to define the functional genomics of key stages of the definitive endoderm (DE) to HBE-ALI differentiation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

16 Samples

Download data: BW

(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:

Homo sapiens; Mus musculus

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) We show direct conversion of mouse fibroblasts to cells that closely resemble intestinal stem cells (ISCs), through the state of fetal-type progenitor cells, called FIPCs. The induced ISCs (iISCs) exhibit self-renewal capacity and intestinal multi-lineage differentiation potential. Upon transplantation, iFIPCs and iISCs reconstitute colonic and intestinal epithelia, respectively.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

18 Samples

Download data: TXT

(Submitter supplied) In response to polarization cues, cultured Caco-2 cells, a human colon adenocarcinoma-derived cell line, form a polarized epithelium resembling normal enterocytes. We investigated potential signaling mechanisms activated by Caco-2 cells that might trigger the genome-wide transcriptional reprogramming that accompanies polarization (Saaf et al, submitted-I). cDNA microarrays were used to compare the transcriptional profile of Caco-2 polarization to the gene expression profiles of normal human colon and colon tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL3526 GPL3335 GPL5067

24 Samples

Download data

(Submitter supplied) CELL CULTURE: The human intestinal epithelial cell line Caco-2 (obtained from Dr. Stanley Falkow, Stanford University) was used to study the genome-wide expression program underlying the transition from cell proliferation to establishment of a polarized epithelial layer. Cells were first grown in sparse culture on plastic p15 dishes to generate a population of "contact naive" cells. These cells were combined and plated at confluency on Costar filter inserts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5058

43 Samples

Download data: PDF

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL18573

13 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) we established a human intestinal stem cell (ISC) culture method expanded under feeder-free and fully defined conditions through selective enrichment of ISC populations (ISC3D-hIO) within hIO derived from human pluripotent stem cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: MTX, TSV

(Submitter supplied) we established a human intestinal stem cell (ISC) culture method expanded under feeder-free and fully defined conditions through selective enrichment of ISC populations (ISC3D-hIO) within hIO derived from human pluripotent stem cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) Background & Aims: Aspirin (ASA) is a proven chemoprotective agent for colorectal cancer; yet, mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. Here, we utilize human colonic organoids to profile ASA responses on genome-wide gene expression and chromatin accessibility. Methods: Human colonic organoids from one individual were cultured and treated in triplicate with 3mM ASA or vehicle control (DMSO) for 24 hours. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL24676

12 Samples

Download data: NARROWPEAK, RESULTS

(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) Mutations in the FOXA1 transcription factor define a unique subset of prostate cancers but the functional consequences of these mutations and whether they confer gain or loss of function is unknown. By annotating the FOXA1 mutation landscape from 3086 human prostate cancers, we define two hotspots in the forkhead domain: Wing2 (~50% of all mutations) and R219 (~5%), a highly conserved DNA contact residue. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

20 Samples

Download data: BW