GEO DataSets

(Submitter supplied) We report that repeated rounds of media submergence damage of human colon organoids led to the inability of cells to regrow and respond appropriately to TLR stimulation. We also identified mRNA expression and DNA methylation changes in genes associated with IBD and colon cancer.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) Acute damage to the intestinal epithelium can be repaired via de-differentiation of mature intestinal epithelial cells to a stem cell state, but there is a lack of knowledge on how these stem cells function after chronic injury, such as in inflammatory bowel disease (IBD). We developed a chronic injury model in human colonoid monolayers by repeated rounds of air-liquid interface and submerged growth. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

12 Samples

Download data: CSV, IDAT

(Submitter supplied) The intestinal epithelium is an immunologically active barrier adapted for a low oxygen environment. Its role is implicated in the pathophysiology of various diseases, including inflammatory bowel disease (IBD) and colorectal cancer. Patient-derived intestinal epithelial organoids (IEOs) mimic the architecture and cell type composition of the intestine and can be used for disease modeling and personalized drug screening. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: SF

(Submitter supplied) Treatment of inflammatory bowel disease (IBD) is challenging, with a series of available drugs each helping only a fraction of patients. Patients may face time-consuming drug trials while the disease is active, thus there is an unmet need for biomarkers and assays to predict drug effect. It is well known that the intestinal epithelium is an important factor in disease pathogenesis, exhibiting physical, biochemical and immunologic driven barrier dysfunctions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

36 Samples

Download data: SF

(Submitter supplied) Gene expression changes of human colon orgnaoids by 60weeks of inflammatory stimulation in vitro (long-term inflammed organoids) and after 10weeks from the removal of stimulation (inflammation-removed organoids). GSEA analysis was performed about RNA1-9 (Organoids #1). For the reproducibility of the analysis, GSEA was performed in triplicate. The key molecule for long-term inflammation was extracted from RNA10-12 (Organoids #2). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20844

15 Samples

Download data: TXT

(Submitter supplied) Purpose: Transcriptomic exploration for the identification of genes induced upon TGR5 stimulation in intestinal stem cells Methods: For each biological replicate, GFPhi cells were isolated by FACS from intestines from 4 pooled Lgr5-eGFP-IRES-CreERT2 mice. About 200.000 GFPhi cells were then embedded in Matrigel (20.000 per well in 10µL Matrigel drop) and after 4 hours were treated with INT-777 (30µM) or DMSO as control. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

6 Samples

Download data: TAB

(Submitter supplied) A human colon carcinoma-derived cell line LS174T was modified to overexpress NICD, intracellular domain of Notch1, upon doxycycline addition (designated as LS174T-tetON-NICD cells), using the T-rex system (Invitrogen). We have previously shown that these cells can overexpress NICD under the control of CMV promoter (Okamoto R et al, Am J Physiol, 296(1):G23-35, 2009), and the amont of the overexpressed NICD protein reaches to the maximal level in early as 3 hours from doxycycline addition (100ng/ml), which persists for up to 24 hours. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13915

3 Samples

Download data: TXT

(Submitter supplied) The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. Our understanding of how this process occurs is limited by a lack of in vitro models that recapitulate key aspects of in vivo responses. We established a long-term, self-organizing 2D epithelial monolayer system to model the cyclic nature of epithelial alterations during injury-repair. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

31 Samples

Download data: TXT

(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