GEO DataSets

(Submitter supplied) To investigate the detailed molecular mechanisms for the regulatory role of HIF-2α in experimental colitis, microarray gene expression analysis was performed on colon RNA isolated from 6- to 8-week-old Hif-2αF/F, Hif-2αlΔIE mice treated with 3%DSS for 3 days. Background & Aims: Hypoxic inflammation is characterized by decreased oxygen tension in inflammatory foci, and is a notable feature in inflammatory bowel disease (IBD). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

2 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

(Submitter supplied) The human C-type lectin Reg3a (HIP/PAP) is an antimicrobial peptide that kills Gram-positive bacteria. Reg3a preserves gut microbiota homeostasis, reinforces intestinal barrier function and thereby helps to fight induced colitis in mice. Transcriptomic data revealed an upregulation of numerous genes involved in the robustness of the intestinal barrier, and the biosynthesis pathway of mucin core 1 and 3 O-glycans.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

35 Samples

Download data: CEL

(Submitter supplied) To investigate the detailed molecular mechanisms for the regulatory role of HIF-1α in colon, microarray gene expression analysis was performed on colon RNA isolated from 6- to 8-week-old Hif-1α+/+, Hif-1αLSL/LSL mice. Background & Aims: The progression and growth of solid tumors leads to a state where tumors outgrow their capacity for efficient oxygenation and nutrient uptake and an increase in tumor hypoxia. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11533

2 Samples

Download data: CEL

(Submitter supplied) Background & Aims Activation of the transcription factor nuclear factor-κB (NF-κB) has been associated with the development of inflammatory bowel disease (IBD). Copper metabolism MURR1 domain containing 1 (COMMD1), a regulator of various transport pathways, has been shown to limit NF-κB activation. We investigated the roles of COMMD1 in the pathogenesis of colitis in mice and IBD in human beings.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

12 Samples

Download data: TXT

(Submitter supplied) By comparing Sirt6-silenced YAMC cells to siControl-transfected YAMC cells, we found that there were 916 and 1,026 differentially expressed genes in the naïve and TNF-a treatment conditions respectively. We also found that there were 302 genes that were co-expressed differentially in both naïve and TNF-a treatment conditions between Sirt6-silenced and siControl-transfected YAMC cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: XLSX

(Submitter supplied) We generated conditional knockout of MHCII in intestinal epithelial cells in C57BL/6 mice (I-AbΔIEC) and compared their colonic transcriptome in control and Citrobacter rodentium infected mice. I-AbWT or I-AbΔIEC mice were orally gavaged with Citrobacter rodentium DBS100

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

12 Samples

Download data: CEL

(Submitter supplied) The transcription factor NF-E2-related factor 2 (Nrf2) is a major modulator of the cellular antioxidant response. To study the role of Nrf2 on mucosal inflammation we used transgenic mice expressing a constitutively active Nrf2 in epithelial cells and induced mucosal inflammation by administration of dextran sulfate sodium. Genome wide expression was studied by mRNA sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

24 Samples

Download data: TXT

(Submitter supplied) We compared the transcriptional signatures of the colonic mucosa from control mice (WT) versus mice deficient for the epithelial pantetheinase Vnn1 (Vnn1KO) or overexpressing Vnn1 specifically in intestinal epithelial cells (VIVA transgenic mice), during the development of DSS-induced colitis.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

30 Samples

Download data: CEL

(Submitter supplied) Studying the variations in VNN1 expression at different stages of the disease and under therapy,

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

39 Samples

Download data: TXT

(Submitter supplied) Ste20-related proline/alanine rich kinase (SPAK) is involved in diverse function, such as the pathogenesis of inflammatory bowel diseases. It is very important to study the underlying mechanisms by which SPAK regulates the progress of IBD. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6780

2 Samples

Download data: TXT

(Submitter supplied) Methods: Colon tissue from 8-10-Week wild-type (WT) and miR-7 deficiency mice with DSS treatment, and miR-7 inhibitor/NC-transfected-FHC cells and Erlotinib plus miR-7 inhibitor-transfected-FHC cells with LPS treatment, mRNA profiles of which were generated by deep sequencing, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

7 Samples

Download data: TXT

(Submitter supplied) Oral administration of dextran sulfate sodium (DSS) to mice induces ulceration and inflammation in the colons of mice. These changes are somewhat similar to those seen in human inflammatory bowel disease. Here we provide a full transcriptome (RNA-Seq) analysis of different gastrointestinal tissues in the regions affected by the DSS chemical, at different timepoints during the injury-inflammation-recovery cycle. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

66 Samples

Download data: CSV

(Submitter supplied) We have identified a squamous epithelium that repairs the distal colon of mice after injury and colitis. Lineage tracing studies demonstrate that this squamous epithelium is derived from a small zone of transitional cells located at the squamocolumnar junction of the rectum and anus. To characterize the molecular properties of this junctional epithelium in homeostasis, colitis, and regeneration, we profiled the distal colon and anus of mice using single-cell RNA-Seq. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

3 Samples

Download data: MTX, TXT

(Submitter supplied) Nlrp6-/- lamina propria Ly6C-hi monocytes in response to AOM/DSS have deficient TNFα production, but increased production of other pro-inflammatory cytokines as compared to WT NLRP6 is a member of the Nod-like receptor family, whose members are involved in the recognition of microbes and/or tissue injury. NLRP6 was previously demonstrated to regulate the production of IL-18 and is important for protecting mice against chemically-induced intestinal injury and colitis-associated colon cancer. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17400

2 Samples

Download data: CEL

(Submitter supplied) Innate lymphoid cells (ILCs) are critically involved in intestinal adaptation to microenvironmental challenges (Colonna, 2018; Guendel et al., 2020) and the gut mucosa is characterized by low oxygen. Adaptation to low oxygen is mediated by Hypoxia-inducible transcription factors (HIFs) the HIF-1α subunit shapes the ILC phenotype upon acute experimental colitis and contributes to intestinal damage. However, the impact of HIF signaling in NKp46+ ILC in the context of repetitive mucosal damage and chronic inflammation, as it typically occurs during inflammatory bowel disease, is unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: LOOM, MTX, TSV

(Submitter supplied) To define the mechanisms that underlie regeneration driven by EP4+ macrophages, we transcriptionally compared the WT and Csf1r-EP4-/- mature macrophages isolated from colon by 39 days post DSS treatment.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

11 Samples

Download data: TXT

(Submitter supplied) Intestinal epithelial cells exist in physiological hypoxia, leading to hypoxia-inducible factor (HIF) activation and supporting barrier function and cell metabolism of the intestinal epithelium. In contrast, pathological hypoxia is a common feature of some disorders, including inflammatory bowel disease (IBD). This work was aimed at studying HIF-associated changes in the intestinal epithelium in IBD. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

9 Samples

Download data: TSV

(Submitter supplied) To uncover hypoxia-induced miRNA-mRNA interactions landscape in colorectal cancer cell lines we performed integrated miRNA/mRNA sequencing of Caco-2 and HT-29 cells. Hypoxia was chemically induced via 24 h cobalt(II) chloride and oxyquinoline treatments.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21697

36 Samples

Download data: TSV

(Submitter supplied) Mucosal healing is a key treatment goal for inflammatory bowel disease, and epithelial regeneration is required for an intact gut epithelium. Long noncoding RNAs are involved in the development of inflammatory bowel disease. Here, we investigated the role of a novel long noncoding RNA, Gm31629, in epithelial regeneration. We used RNA-seq to to detail the global programme of gene expression in distal colon tissues from WT and Gm31629-/-.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT