Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole blood expression profiling of patients with inflammatory bowel diseases in IBD-Character cohort

ABSTRACT: The IBD-Character cohort (Edinburgh, Oslo, Örebro, Linköping, Zaragoza, Maastricht) included patients with inflammatory bowel diseases (IBD: Crohn's disease, ulcerative colitis) recruited at diagnosis and non-IBD controls. Paired-end RNA sequencing was used for whole blood expression profiling. Raw and normalized counts tables are provided.

INSTRUMENT(S): unspecified

ORGANISM(S): Homo sapiens

SUBMITTER: Jonas Halfvarson

PROVIDER: E-MTAB-11349 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections

Project description:Peripheral blood-derived macrophages were stimulated with viral-like particles isolated from colonic resections from patients with Crohn's disease (CD), ulcerative colitis (UC), or non-IBD controls diagnoses. RNAseq was performed to unbiasedly assess the transcriptional responses to these stimuli and revealed highly divergent macrophage transcriptional programs in response to non-IBD compared to IBD VLP.

2020-06-01 | GSE135223 | GEO

Transcriptional profiling of human paediatric CD8+ T-cells in Inflammatory Bowel Diseases

Project description:Differences in CD8+ T-cell expression have previously been reported to correlate with disease outcome in adult patients diagnosed with Inflammatory Bowel Diseases (IBD). In addition, T-cell exhaustion was found to be associated with a milder disease course in adults. The purpose of this study was to test the prognostic value of the reported adult T-cell expression and exhaustion signatures in a cohort of children newly diagnosed with Crohn's disease (CD) and ulcerative colitis (UC). We also investigated the possibility of a paediatric specific prognostic expression signature.

2019-09-01 | E-MTAB-7923 | biostudies-arrayexpress

Crohn's Disease patients and non-IBD controls : ileal gene expression

Project description:Comparison of gene expression from ileal biopsies of Crohn's Disease patients and non-IBD controls

2022-12-30 | E-MTAB-10395 | biostudies-arrayexpress

Transcriptomic profiling of THP-1 stable cell lines overexpressing genes associated with inflammatory bowel diseases (IBD)

Project description: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. An empty vector transduced into THP-1 as control. Three biological replicates have been done for each transduction. The impact of each IBD ORFs on THP-1 transcriptome profile was analyzed using an whole RNA sequencing-based approach. This functional genomics screen showed the affected genes (upregulated and downregulated) in response to the increased expression RNA of each IBD gene (ORF) in THP-1. In order to find biological categories enriched of the affected genes, enrichment analyses have been done using the g:GOSt functional profiling tool (using Ensembl database release 98) from the online g:Profiler service.

2022-09-06 | GSE175685 | GEO

RNA-sequencing of inflamed intestinal mucosa of inflammatory bowel disease patients

Project description:Studying differences in responders and non-responders to therapy in inflammatory bowel disease (IBD) patients (crohn's disease and ulcerative colitis)

2019-01-24 | E-MTAB-7604 | biostudies-arrayexpress

Ileum Transcriptomic Profiling in Inflammatory Bowel Disease

Project description:We report ileum gene expression of 37 controls and 158 patients with either Crohn's disease (n=112), ulcerative colitis (n=44), unclassifed IBD (1), or IBS (1). We contrast gene expression in African American (n=104) versus white (n=25) CD and UC patients.

2020-04-15 | GSE137344 | GEO

The transcription start site and enhancer landscape of the descending colon in inflammatory bowel disease

Project description: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. Here, we profiled genome-wide promoter and enhancer activity in the descending colon of IBD patients. IBD-induced enhancer and promoters are highly enriched for IBD-associated SNPs, and can predict IBD diagnosis with an accuracy of 85% in an external cohort.

2018-03-14 | GSE95437 | GEO

Deep metaproteomics of inflammatory bowel diseases

Project description:Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is associated with a loss or an imbalance of host-microbe interactions. Depletion-assisted deep metaproteomics was employed to reveal disease-specific networks of host-microbial protein associations in IBD.

2023-06-28 | PXD043380 | iProX

Functional characterization of inflammatory bowel disease-associated gut dysbiosis in gnotobiotic mice

Project description:Gut dysbiosis is closely involved in the pathogenesis of inflammatory bowel disease (IBD). However, it remains unclear whether IBD-associated gut dysbiosis plays a primary role in disease manifestation or is merely secondary to intestinal inflammation. Here, we established a humanized gnotobiotic (hGB) mouse system to assess the functional role of gut dysbiosis associated with two types of IBD - Crohn's disease (CD) and ulcerative colitis (UC). In order to explore the functional impact of dysbiotic microbiota in IBD patients on host immune responses, we analyzed gene expression profiles in colonic mucosa of hGB mice colonized with healty (HC), CD, and UC microbiota.

2015-10-10 | GSE73882 | GEO

Whole Blood Transcriptome Profiling in Juvenile Idiopathic Arthritis and Inflammatory Bowel Disease

Project description: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.

2018-05-29 | GSE112057 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data