GEO DataSets

(Submitter supplied) Ribo-zero RNAseq experiments were carried out with mouse distal colon DSS Colitis model of genetically engineered mice. For each mouse line for: Gpsm3 (3% DSS), Aif1 (3% DSS), Nckap1l (Hem1), Dock2 (3% DSS), Dok3 (3.5% DSS) DSS treatment for five days followed by water for 5 days, (7 days for Nckap1l). Tissue was collected at Day 10 (Day 12 for Nckap1l (HEM1)).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

194 Samples

Download data: TXT

(Submitter supplied) Microarray Analysis of Human Whole Blood and Intestinal Biopsy Samples from a Phase 2b, Multicenter, Randomized, Double-blind, Placebo-controlled, Parallel-group Study of Ustekinumab in Crohn’s Disease

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13158

1717 Samples

Download data: CEL

(Submitter supplied) This study focuses on inflammatory bowel disease gene expression profiling. Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

134 Samples

Download data: TXT

(Submitter supplied) Background & Aims: The contribution of genetics to the pathogenesis of inflammatory bowel disease (IBD) has been established by twin studies, targeted sequencing and genome-wide association studies (GWASs). This has yielded a plethora of risk loci with an aim to identify causal variants. Research on the genetic components of IBD has mainly focused on protein coding genes, thereby omitting other functional elements in the human genome i.e. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16558

8 Samples

Download data: COD, TXT

(Submitter supplied) Background: Genome wide association studies (GWASs) have revealed many susceptibility loci for complex genetic diseases. For most loci the causal genes have not been identified. The identification of candidate genes is currently mainly based genes that localize close to or within the identified loci. We have recently shown that 92 of the 163 Inflammatory Bowel Disease (IBD)-loci co-localize with noncoding DNA regulatory elements (DRE). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

372 Samples

Download data: WIG

(Submitter supplied) Identification of genes differentially expressed in inflamed and intact colon samples of TNBS treated in vivo rat model of Inflammatory Bowel Disease

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16312

14 Samples

Download data: XLSX

(Submitter supplied) Background: Genetic studies have been tremendously successful in identifying genomic regions associated with a wide variety of phenotypes, although the success of these studies in identifying causal genes, their variants, and their functional impacts have been more limited.   Methods: We identified 145 genes from IBD-associated genomic loci having endogenous expression within the intestinal epithelial cell compartment.  We evaluated the impact of lentiviral transfer of the open reading frame (ORF) of these IBD genes into the HT-29 intestinal epithelial cell line via transcriptomic analyses.  Comparing the genes whose expression was modulated by each ORF, as well as the functions enriched within these gene lists, identified ORFs with shared impacts and their putative disease-relevant biological functions. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

376 Samples

Download data: TXT

(Submitter supplied) Background: Genetic studies have been tremendously successful in identifying genomic regions associated with a wide variety of phenotypes, although the success of these studies in identifying causal genes, their variants, and their functional impacts have been more limited.   Methods: We identified 145 genes from IBD-associated genomic loci having endogenous expression within the intestinal epithelial cell compartment.  We evaluated the impact of lentiviral transfer of the open reading frame (ORF) of these IBD genes into the HT-29 intestinal epithelial cell line via transcriptomic analyses.  Comparing the genes whose expression was modulated by each ORF, as well as the functions enriched within these gene lists, identified ORFs with shared impacts and their putative disease-relevant biological functions. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL30867

426 Samples

Download data: TXT

(Submitter supplied) To investigate whether the H3K27ac is involved in the development of inflammatory bowal disease. We established dextran sulfate sodium (DSS)-induced chronic colitis and performed RNA-sequencing and Chromatin Immunoprecipitation followed by NGS sequencing for H3K27ac in the mice colon tissues. We find that the global H3K27ac distribution in colon tissue had no significant difference, while on the typical-enhancers specific in the DSS group, H3K27ac signals were significantly enriched when compared with the control. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BW

(Submitter supplied) Anti-TNF induced macrophages from MLR (6) were compared to IFNγ (6), IL-4 (6) and IL-10 (6) polarized macrophage subsets.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

24 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: It has been found that miR-21 is increased in colonic tissues and decreased in peripheral blood regulatory T cells (Tregs) of patients with ulcerative colitis (UC). We aimed to investigate the influence of miR-21 on Tregs function in intestinal inflammation. Methods: Various CD4+ T cell populations were flow-cytometry sorted from miR-21-/- mice and littermates (WT) utilization in T-cell transfer colitis model and suppression of T cell activation and proliferation by Tregs. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

8 Samples

Download data: TXT

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

Organism:

Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human immunodeficiency virus 1; Rattus norvegicus; Murid betaherpesvirus 1; JC polyomavirus; Homo sapiens; Murid gammaherpesvirus 4; Betapolyomavirus hominis; human gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus macacae

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL6885 GPL7723

26 Samples

Download data

(Submitter supplied) Background: MicroRNAs (miRNAs) acting as negative regulators of gene expression are differentially expressed in intestinal tissues of patients with inflammatory bowel disease (IBD). Assessing the functional role of miRNAs in murine models of colitis facilitates elucidating the role of specific miRNAs in human IBD. The aim of this study was to determine the miRNA signature of murine models of colitis and to assess the influence of miR-21 on intestinal inflammation. more...

Organism:

Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Homo sapiens; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Rattus norvegicus; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae

Type:

Non-coding RNA profiling by array

Platform:

GPL7723

8 Samples

Download data: TXT

(Submitter supplied) Background: MicroRNAs (miRNAs) acting as negative regulators of gene expression are differentially expressed in intestinal tissues of patients with inflammatory bowel disease (IBD). Assessing the functional role of miRNAs in murine models of colitis facilitates elucidating the role of specific miRNAs in human IBD. The aim of this study was to determine the miRNA signature of murine models of colitis and to assess the influence of miR-21 on intestinal inflammation. more...

Organism:

Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Rattus norvegicus; Murid gammaherpesvirus 4; Betapolyomavirus hominis; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae

Type:

Non-coding RNA profiling by array

Platform:

GPL7723

12 Samples

Download data: TXT

(Submitter supplied) Background: MicroRNAs (miRNAs) acting as negative regulators of gene expression are differentially expressed in intestinal tissues of patients with inflammatory bowel disease (IBD). Assessing the functional role of miRNAs in murine models of colitis facilitates elucidating the role of specific miRNAs in human IBD. The aim of this study was to determine the miRNA signature of murine models of colitis and to assess the influence of miR-21 on intestinal inflammation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

6 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13607

68 Samples

Download data: TXT

(Submitter supplied) Genome wide transcriptional profiles of biopsies collected from non-IBD control subjects

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13607

27 Samples

Download data: TXT

(Submitter supplied) The MUCUS clinical trial (https://clinicaltrials.gov: NCT01433471) was established to investigate the effect of Trichuris suis ova on ulcerative colitis patients.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16699

14 Samples

Download data: TXT

(Submitter supplied) Inflammatory bowel diseases (IBD) are believed to be driven by dysregulated interactions between the host and the gut microbiota. Our goal is to characterize the relationships between mucosal T cells, the host tissue environment and microbial communities in IBD patients to identify new therapeutic targets. We identified 26 predictors from our combined data set that were effective in distinguishing between regions of the intestine undergoing active inflammation and regions that were normal. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13607

41 Samples

Download data: TXT

(Submitter supplied) We generated ATAC-seq and H3K27ac ChIP-seq data in immortalized immune cancer cell lines to predict enhancer-gene regulation using the ABC model.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

67 Samples

Download data: TDF