GEO DataSets

(Submitter supplied) This scRNA-seq dataset of five human subjects with ulcerative colitis (derived from colonic lamina propria samples), was analyzed and published as part of a larger manuscript (Mitsialis, V et al, "“Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease” in Gastroenterology), which reported immune signatures of blood and intestinal tissue differentiating ulcerative colitis from Crohn's disease from non-IBD human subjects using mass cytometry as well as scRNA-seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: CSV, TXT

(Submitter supplied) To determine the differentially expressed genes between these subsets and identify the core human in vivo differentiated Tr1 cell gene signature

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: TXT

(Submitter supplied) Background and Aims: Crohn’s disease [CD] and ulcerative colitis [UC] are distinct forms of inflammatory bowel disease. Heterogeneity of HLA-DR+SIRPα + mononuclear phagocytes [MNPs], including macrophages [MΦ], monocyte-derived [Mono] cells, and dendritic cells [DCs], was reported in gut tissue but not yet investigated in mesenteric lymph nodes [MLNs] of IBD patients. We here compared the phenotype, function, and molecular profile of HLA-DR+SIRPα+ MNPs in CD and UC MLNs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

22 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 5 Crohn's disease affected, 5 ulcerative colitis affected, and 12 normal individuals. One ulcerative colitis sample was assayed before and after treatment with infliximab and mesalamine.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

23 Samples

Download data: TXT

(Submitter supplied) Genome wide expression profiling of ulcerative colitis, and normal colon mucosa samples. The GeneChip PrimeView Human Gene Expression Array was used to obtain expresion profiles across colon mucosa samples. Samples came from 5 ulcerative colitis affected, and 5 normal individuals.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

10 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

73 Samples

Download data

(Submitter supplied) Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 10 Crohn's disease affected, 4 ulcerative colitis affected, and 10 normal individuals. One ulcerative colitis sample was assayed before and after treatment with 6-mercaptopurine and mesalamine.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

25 Samples

Download data: TXT

(Submitter supplied) The complex milieu of inflammatory mediators associated with many diseases is often too dilute to directly measure in the periphery, necessitating development of more sensitive measurements suitable for mechanistic studies, earlier diagnosis, guiding selection of therapy, and monitoring interventions. Previously, we determined that plasma of recent-onset (RO) Type 1 diabetes (T1D) patients induce a proinflammatory transcriptional signature in fresh peripheral blood mononuclear cells (PBMC) relative to that of unrelated healthy controls (HC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

47 Samples

Download data: CEL

(Submitter supplied) Mucosal host DNA methylation was associated with the presence of inflammation suggesting epigenetic changes in response to the microbiota. Hierarchical clustering of the microbiota indicated ten subgroups, whereas some were driven by certain Enterbacteriacae and Bacteroides keystone species, and which were associated with host genotype and DNA methylation profiles, but with little influence from the habitual diet.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

100 Samples

Download data: CSV, IDAT

(Submitter supplied) Vedolizumab (VDZ) is used to treat patients with IBD but the exact way it works is not known. We studied the immune system in the blood and intestine of patients treated with VDZ and found immune characteristics that correlated with response.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

172 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

442 Samples

Download data

(Submitter supplied) Background: Vedolizumab, an antibody blocking integrin α4β7, is a safe and effective therapy for Crohn’s disease and ulcerative colitis. Blocking α4β7 from binding its cognate addressin MAdCAM-1 on intestinal blood vessel endothelial cells prevents T cells from migrating to the gut mucosa in animal models. However, data supporting this mechanism of action in humans is limited. Methods: We conducted a cross-sectional case-control study to evaluate the effect of vedolizumab on intestinal immune cell populations while avoiding the confounding effect resolving inflammation could have on the cellularity of the colonic mucosa in treatment-responsive patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

346 Samples

Download data: CSV

(Submitter supplied) Background: Vedolizumab, an antibody blocking integrin α4β7, is a safe and effective therapy for Crohn’s disease and ulcerative colitis. Blocking α4β7 from binding its cognate addressin MAdCAM-1 on intestinal blood vessel endothelial cells prevents T cells from migrating to the gut mucosa in animal models. However, data supporting this mechanism of action in humans is limited. Methods: We conducted a cross-sectional case-control study to evaluate the effect of vedolizumab on intestinal immune cell populations while avoiding the confounding effect resolving inflammation could have on the cellularity of the colonic mucosa in treatment-responsive patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

96 Samples

Download data: CSV

(Submitter supplied) We explored how the human macrophages response to different inflammatory factors, focusing particularly on the effects of antiviral interferons (IFN-β and IFN-γ), pro-inflammatory cytokines such as TNF-α, and other mediators like IL-4. Co-cultured fibroblasts were a component in some conditions to generate factors produced by resident stroma. We used a single-cell antibody-based hashing strategy to multiplex samples from different stimulatory conditions in one sequencing run. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: H5, RDS

(Submitter supplied) Transcriptomic data was generated on uninvolved SB tissue from formalin-fixed paraffin-embedded (FFPE) small bowel resection margins of subjects requiring surgery at Cedars-Sinai Medical Center for Crohn’s disease.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

314 Samples

Download data: TXT, XLSX

(Submitter supplied) Presenting features of inflammatory bowel disease (IBD) are non-specific. We hypothesized that mRNA profiles could (1) identify genes and pathways involved in disease pathogenesis; (2) identify a molecular signature that differentiates IBD from other conditions; (3) provide insight into systemic and colon-specific dysregulation through study of the concordance of the gene expression. Children (8-18 years) were prospectively recruited at the time of diagnostic colonoscopy for possible IBD. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

176 Samples

Download data: CEL

(Submitter supplied) The mechanisms behind acute mucosal injury responses in humans are poorly investigated.We thus examined the acute responses to mucosal barrier injury in humans with and without UC. A standardized mucosal wound extending to the muscularis mucosa layer was inflicted in the sigmoid colon of 6 patients with quiescent UC and 6 control subjects. Macroscopic, microscopic and molecular injury responses were assessed at 24 and 48 hours by repeated high resolution imaging and collection of biopsies across the wounds which were assessed by RNA sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

36 Samples

Download data: TXT

(Submitter supplied) The pathophysiology of Crohn’s-like disease of the pouch (CDP) that develops after restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC) is unknown. We examined mucosal cells from patients with and without CDP using single cell analyses.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

59 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) RNA-seq analysis of total RNA isolated from laser capture microdissected intestinal epithelium. The analysis aimed at characterizing the epithelial gene expression changes in IBD patients vs. healthy controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

29 Samples

Download data: TXT

(Submitter supplied) Inflammatory bowel disease (IBD) is a common and chronic gut disorder, with two subtypes: Crohn's disease (CD) and ulcerative colitis (UC), which are challenging to diagnose. The molecular pathology IBD is not well understood, and the underlying gene regulatory regions have not been comprehensively investigated. Relatedly, most IBD-associated SNPs are located in non-coding regions, and may effect gene regulation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

94 Samples

Download data: BED