GEO DataSets

(Submitter supplied) Pathological expansion of adipose tissue (AT) is supported by adipocyte precursors, termed adipose-derived stem cells (ASCs). Elucidation of mechanisms underlying ASC function may lead to therapeutic interventions to use in cell therapy treatments on Crohn’s disease patients. Using epigenome-wide association studies, we explored the impact of Crohn’s disease on the methylation signature of human ASCs

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

13 Samples

Download data: IDAT

(Submitter supplied) Genome wide DNA methylation profiling of female Crohn's disease patients versus healthy female controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs in peripheral blood samples. Samples included 25 healthy controls and 18 female patients with histologically confirmed CD.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16304

40 Samples

Download data: IDAT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL11154

66 Samples

Download data: TXT

(Submitter supplied) A genome-wide DNA methylation study was conducted using base resolution bisulfite sequencing for purified intestinal CD4+ cells (resected or biopsied mucosa of a terminal ileum) from 21 patients with Crohn’s disease and 12 age/sex matched controls. The sequencing data was analyzed for differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs). Integration was performed with RNA-sequencing data for the same set of samples to verify the functional impact of DNA methylation changes.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

33 Samples

Download data: TXT

(Submitter supplied) A genome-wide DNA methylation study was conducted using base resolution bisulfite sequencing for purified intestinal CD4+ cells (resected or biopsied mucosa of a terminal ileum) from 21 patients with Crohn’s disease and 12 age/sex matched controls. The sequencing data was analyzed for differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs). Integration was performed with RNA-sequencing data for the same set of samples to verify the functional impact of DNA methylation changes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

33 Samples

Download data: TSV

(Submitter supplied) In Crohn's disease, creeping fat is the characteristic expansion of mesenteric adipose tissue wrapping around the inflamed intestine. Through a comparative transcriptomic analysis of creeping fat and normal-looking mesenteric adipose tissues from patients with Crohn's disease and non-Crohn's disease, we found that a dynamic transcriptional and cell compositional change occurs during the progression from non-Crohn's disease to Crohn's disease, and finally to creeping fat.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

59 Samples

Download data: TXT

(Submitter supplied) Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT

(Submitter supplied) Crohn’s disease is a relapsing inflammatory disorder with a variable clinical course. While most patients present with purely an inflammatory phenotype (B1) at diagnosis, a subgroup (~20%) rapidly progresses to complicated disease manifestations that include stricturing (B2) within 5 years. DNA methylation is a key epigenetic mechanism that can regulate gene expression and thereby influence the development and progression of complex diseases. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

402 Samples

Download data: TXT

(Submitter supplied) Employing microarray assays, a total of 267 genes were identified that were significantly up- or downregulated in PBMCs of WT-NOD2 patients, compared to healthy donors after challenge with vitamin D (+/-D) and/or a combination (+/-LP) of LPS (lipopolysaccharide) and PGN (peptidoglycan) (p < 0.05; threshold: ≥ 2-fold change). For further analysis by real-time PCR, 12 genes with known impact on inflammation and immunity were selected that fulfilled predefined expression criteria. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

24 Samples

Download data: CEL, CHP

(Submitter supplied) The Illumina NextSeq500 was used to sequence the gene expression profiles of 21 ileal fibroblast samples. Samples included 6 control samples and 15 Crohn’s disease samples. The Crohn’s disease samples can be further subdivided into inflamed (4), non-inflamed (6) and stenotic (5) samples. This experiment together was performed in conjunction with a DNA methylation experiment (GSE99788). Use Supplemental Table 2 of the manuscript to quickly find the samples that were present in both experiments.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

21 Samples

Download data: CSV

(Submitter supplied) The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 867,000 CpGs in ileal fibroblast samples. Samples included 5 control samples and 13 Crohn’s disease samples. The Crohn’s disease samples can be further subdivided into inflamed (2), non-inflamed (7) and stenotic (4) samples. This experiment together was performed in conjunction with a gene expression experiment (GSE99816). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

18 Samples

Download data: IDAT, TXT

(Submitter supplied) Purpose: ME/CFS is a lifelong debilitating disease that affects approximately 1% of the global population. Previous studies have identified dysfunctional activity in metabolic, immune and neurological pathways. The goal of this study is to identify ME/CFS specific variations in DNA methylation to determine whether the patient specific epigenetic patterns provide insight into the disease pathophysiology. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

20 Samples

Download data: CSV, TXT, XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL10558 GPL13534

875 Samples

Download data: IDAT, TXT

(Submitter supplied) Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

384 Samples

Download data: IDAT, TXT

(Submitter supplied) Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

240 Samples

Download data: IDAT, TXT

(Submitter supplied) Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

251 Samples

Download data: IDAT, TXT

(Submitter supplied) Tissue fibrosis is a serious complication of Crohn’s disease (CD) as well as of a variety of other complex, chronic pathologies. Understanding the underlying pathophysiology of tissue fibrosis is crucial for the development of tissue-specific prevention and interventional treatment strategies. To identify molecular states specific to fibrotic disease, we employed deep sequencing to define the genome-wide DNA methylome and the whole transcriptome of purified human intestinal fibrotic fibroblasts (HIFs) isolated from the colon of patients with fibrotic CD. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791

12 Samples

Download data: TXT

(Submitter supplied) Previously, we conducted an epigenome-wide study of DNA methylation (~850K sites) in peripheral blood at diagnosis and during follow-up from the RISK pediatric Crohn’s disease inception cohort and data are deposited in GEO with an access number GSE112611. We further followed up this study and identified here the genetic influence on ~850K DNAm sites (mQTL) in peripheral blood as well as newly added 41 ileal biopsies. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

41 Samples

Download data: IDAT

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL23126 GPL13534

31 Samples

Download data: CEL, IDAT

(Submitter supplied) Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue. Our aim was to investigate differential DNA methylation correlated to gene expression in relation to survival data.We sought to identify aberrant DNA methylation of genes that could be linked to metastatic disease and poor survival. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

8 Samples

Download data: CEL