GEO DataSets

(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) 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) We performed promoter Capture Hi-C in HepG2 to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We also performed ChIP-Seq at 2h, 8h and 23h timepoints in HepG2 for Il1B treatment.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL11154

10 Samples

Download data: BIGWIG, TXT

(Submitter supplied) The demonstration that chromatin exhibits a complex 3 dimensional organization, whereby short and long distance physical interactions correspond to complex gene regulatory processes has opened a new window on understanding the functional organization of the human genome. Recently, chromatin remodeling has also been causally implicated in several neurodevelopmental disorders, including autism and schizophrenia. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

6 Samples

Download data: BED, HDF5

(Submitter supplied) GWAS have discovered thousands of genomic loci that are associated with disease risk and quantitative traits, but most of the variants responsible for risk remain uncharacterized. The vast majority of GWAS-identified loci contain non-coding SNPs and defining molecular mechanism of risk is challenging. Many non-coding causal SNPs are hypothesized to alter Transcription Factor (TF) binding sites as the mechanism by which they affect organismal phenotypes. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

5 Samples

Download data: BED, BEDGRAPH, BIGWIG

(Submitter supplied) Maps of open chromatin in three primary human blood cell types of the myeloid lineage (megakaryocytes, erythroblasts and monocytes) using the formaldehyde-assisted isolation of regulatory elements method followed by next-generation sequencing (FAIRE-seq). We also generated FAIRE-seq data in the megakaryocytic cell line CHRF-288-11. In addition to our data sets, we retrieved FAIRE-seq data for the erythroblastoid cell line K562 (ENCODE Project Consortium 2012) and pancreatic islets (Gaulton et al. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL10999 GPL9115

6 Samples

Download data: BED

(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) Application of Systems Genetics analysis for systematic evaluation of candidate causal genes associated with risk of Type 1 Diabetes along with follow-up bioinformatics pathway analysis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

590 Samples

Download data: TXT

(Submitter supplied) Genome wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

40 Samples

Download data: TXT

(Submitter supplied) We report ileal gene expression at diagnosis in a cohort of 210 treatment-naïve patients of pediatric Crohn's disease and 35 non-IBD controls from the RISK study. After three years of follow-up after diagnosis, 27 of the CD patients progressed to complicated disease (B2 and/or B3). We aim to test whether Transcriptional Risk Scores helps to distinguish between patient subgroups, improving the predictive power gained from Genetic Risk Scores.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

245 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:

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) Objective The imbalance between Th17 cells and regulatory T cells in the gut of inflammatory bowel disease (IBD) patients promotes intestinal epithelial cell damage. In this scenario, T helper cell lineage commitment is accompanied by dynamic changes to the chromatin that facilitate, enforce or repress gene expression patterns and ultimately promote the induction and maintenance of dysregulated intestinal CD4 T cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) For Large White (LW) and Meishan (MS) skeletal muscle, we performed H3K27ac BL HiCHIP to establish enhancer-promoter interaction maps. We also performed GRID-seq which uses a bivalent linker to ligate RNA to DNA in situ.

Organism:

Sus scrofa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19176

12 Samples

Download data: BEDPE, MCOOL, TXT

(Submitter supplied) Although major advances in genomics have initiated an exciting new era of research, the lack of information about cis-regulatory elements has limited the genetic improvement or manipulation of pig as meat source and biomedical model. Here, we systematically characterize the cis-regulatory elements and their functions in the pig genome in 12 diverse tissues from 4 pig breeds through RNA-Seq, ATAC-Seq, and ChIP-Seq analyses. more...

Organism:

Sus scrofa

Type:

Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22918

200 Samples

Download data: BED, BEDGRAPH, BIGWIG, NARROWPEAK

(Submitter supplied) We report whole blood gene expression of 12 healthy controls and 190 patients with either oligoarticular (n=43), polyarticular (n=46), or systemic JIA (n=26), or Crohn's disease (n=60) and ulcerative colitis (n=15). The subtypes of JIA are characterized by a gradient of differential gene expression ranging from controls to oligoJIA, polyJIA, sJIA, and IBD.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

202 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

(Submitter supplied) More than 200 genomic loci have been identified and validated by GWAS to be associated with IBD. However, for most of these loci, the causal gene remains unknown. The current study is aimed at uncovering the role of genes located within IBD-associated loci and endogenously expressed in the myeloid cell model THP-1 by over-expressing them in this cell lineage. The open reading frames (ORF) for 42 genes from IBD-associated loci were expressed in the THP-1 model of human monocytes using lentivirus vector for plasmid transduction. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

143 Samples

Download data: TXT

(Submitter supplied) Transcriptome data measured by microarray in colon of the BXD mouse genetic diversity model under a standard chow or a high fat diet at a fastd state.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

99 Samples

Download data: CEL

(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