GEO DataSets

(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) 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) 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 GPL19057

7 Samples

Download data: BW, TXT

(Submitter supplied) To identify the potential genes that regulated by Ezh2, we immunoprecipitated chromatin from macrophages stimulated with or without LPS, and analyzed the precipitated DNA with deep sequencing (CHIP-Seq).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BED, BW

(Submitter supplied) we conducted gene expression profile analysis by using WT and Ezh2-deficient bone marrow-derived macrophages.Gene ontology (GO) analysis revealed the most prominent biological processes altered in macrophages upon LPS stimulation were associated with immune system process.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: TXT

(Submitter supplied) To test the efficacy of TNFR-Fc and anti-TWEAK mAb treatment alone and in combination Tumor necrosis factor (TNF)-alpha is a major effector in various inflammatory conditions. TNF-like weak inducer of apoptosis (TWEAK) is a member of the TNF superfamily that promotes inflammatory tissue damage through its receptor, FGF-inducible molecule 14 (Fn14). Since both TWEAK and TNF-alpha have been shown to mediate pathological responses through inter-dependent or independent pathways by in vitro, the potential interplay of these pathways was investigated in a mouse colitis model. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

72 Samples

Download data: CEL

(Submitter supplied) Background and Aims: Individuals with ulcerative colitis (UC) are at increased risk for colorectal cancer, although underlying mechanisms are incompletely understood. We sought to identify a potential gene expression signature in non-dysplastic distal mucosa that as a “genetic field effect” could be a marker for remote neoplastic lesions. Results: 468 genes were significantly up-regulated and 541 genes were significantly down-regulated >2-fold in UC patients with neoplasia compared to UC patients without neoplasia. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13158

20 Samples

Download data: CEL

(Submitter supplied) Regulation of epithelial barrier function is dependent upon precise control of cell survival and activation of inflammatory pathways in response to the enteric flora. These experiments tested differential colon gene expression relative to these pathways in wild type and STAT5b deficient mice. Keywords: Single time point in wild type and STAT5b deficient mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3385

Platform:

GPL5759

8 Samples

Download data: CEL

Analysis of colons of animals lacking the Signal Transducers and Activators of Transcription member STAT5b. STAT5b mutants are more susceptible to experimental colitis, associated with intestinal barrier function defects. Results provide insight into the role of STAT5b in colonic barrier function.

Organism:

Mus musculus

Type:

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

Platform:

GPL5759

Series:

GSE8942

8 Samples

Download data: CEL

(Submitter supplied) Long non-coding RNAs (lncRNAs) are central regulators of the inflammatory response and play an important role in inflammatory diseases. PINT has been reported to be involved in tissue development and tumorigenesis. However, potential functions of PINT in the innate immune system are largely unknown. Here, we report a specific role for PINT in activating inflammatory gene transcription. The expression of PINT is primarily dependent on the NF-κB signaling pathway in macrophages and intestinal epithelial cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

15 Samples

Download data: TXT

(Submitter supplied) Athough anti-TNF therapies can be used to treat colitis associated with inflammatory bowel disease, in mice the loss of the TNF receptor TNFR1 (Tnfrsf1a) in the Il10-/- spontaneous colitis background results in acceleration of disease onset. Whereas Il10-/- mice on the Bl/6 background are relatively protected from colitis throughout life, Il10-/- Tnfr1-/- mice develop colitis beginning at 4 wks of age. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

11 Samples

Download data: CSV

(Submitter supplied) The loss of TNFR1 (Tnfrsf1a) in the Il10-/- spontaneous mouse colitis background results in acceleration of disease onset. Whereas Il10-/- mice on the Bl/6 background are relatively protected from colitis throughout life, Il10-/- Tnfr1-/- mice develop colitis beginning at 4 wks of age. Their disease results in nearly 50% mortality by 12 wks of age. We hypothesized that this early-onset colitis was due to dysregulation of immune signals in early life, defining a key period known as the "weaning reaction" in which proinflammatory signals help induce mucosal tolerance of the microbiome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: CSV

(Submitter supplied) We have compared mRNA expression in full-thickness mouse colon between wildtype mice and mice with a genetic deletion in tumor necrosis factor receptor 1 (TNFR1, encoded by the Tnfrsf1a gene). This experiment was motivated by our observation that Il10-/- Tnfr1-/- double-knockout mice develop very-early-onset colitis at the time of weaning, significantly earlier than disease onset in Il10-/- single-knockout mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) We wanted to understand the consequences of GSK126-mediated Ezh2 inhibition in an orthotopic model of Kras-driven non-small cell lung cancer (NSCLC). We injected the NSCLC cells with above-mentioned genotype into Nude mice and treated them with GSK126 50mg/kg (daily) or vehicle. As additional control for Ezh2 specificity we treated one tumor with doxycycline that induces shRNA-mediated Ezh2 protein downregulation in those cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057

18 Samples

Download data: BW, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL16686

10 Samples

Download data: CEL

(Submitter supplied) To investigate the novel function TRIM40 in intestinal epithelial cells, we established TRIM40 overexpressing HT-29 cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) To identify the differentially expressed genes by TRIM40 overexpression in intestinal cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

6 Samples

Download data: CEL, XLSX

(Submitter supplied) A member of the nuclear receptors, retinoic acid-related orphan receptor a (RORa) is an important transcription factor for various biological processes including circadian rhythm, metabolic regulation, immune cell development and cancer. Here we found that RORa is important for intestinal homeostasis by negatively regulating the transcriptional activity of NF-kB, a major inflammatory regulator in intestinal epithelial cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TXT

(Submitter supplied) Cutaneous squamous cell carcinoma (cSCC) is the second most common malignancy in humans and approximately 5% metastasize, usually to regional lymph nodes. Epigenetic regulation of gene expression may allow tumoral cells to acquire new functions in order to escape from the primary tumor. The aim of this study was to investigate the expression and function of proteins of the Polycomb family of epigenetic regulators in the metastatic process of cSCC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

8 Samples

Download data: CEL