Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reveal the key mediators of inflammation in Crohn's disease undergoing biological treatments

ABSTRACT: Reveal the key mediators of inflammation in Crohn's disease undergoing biological treatments

PROVIDER: PRJNA1107958 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28903000_1.fastq.gz	Fastqsanger.gz
	SRR28903000_2.fastq.gz	Fastqsanger.gz
	SRR28903100_1.fastq.gz	Fastqsanger.gz
	SRR28903100_2.fastq.gz	Fastqsanger.gz
	SRR28903001_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 316

Similar Datasets

Reveal the key mediators of inflammation in Crohn's disease undergoing biological treatments

Project description:Crohn’s disease (CD) is a major subtype of life-long Inflammatory Bowel Disease (IBD) affecting a growing population in United States. To advance the knowledge in pathology, our study investigates into the common inflammatory feature in CD across different inflammation statuses by single-cell transcriptomics. First, we provided a detailed mucosal cellular landscape of terminal ileum (TI) and ascending colon (AC), with endoscopic diagnosis (CD inflamed, adjacent-to-inflamed, non-inflamed and non-IBD control), including a cohort of patients undergoing biological treatments. Differences between regions (TI and AC), and features of mucosal inflammation status in cellular composition are captured within the cellular landscapes. Second, we identified an inflammation cascade that include follicle-associated enterocytes and macrophages via molecules like CCL20 and S100As, as key mediators of CD inflammation. These key mediators serve as hubs in imputed cell-cell interactions under CD inflammation, expanding the interplay network with increasing disease severity. Finally, we demonstrate a scoring method by surveying the mucosa, using GWAS loci, and transcriptome features including differentially expressed genes (DEGs), and genes from a novel singular value decomposition (SVD)-based co-expression network analysis framework. Applying independently to the epithelial and immune lineage, we identify inflammation signatures that reflect disease severity. Furthermore, we report a short, robust list of epithelial and immune transcript makers whose expressions harmonize with endoscopic diagnosis and histological assessment. These markers are merely within known IBD GWAS loci. Collectively, this study narrates a shared inflammation pattern involving cells and cytokines for active CD and present a short list of markers for metrical inflammation assessment.

2024-12-16 | GSE266616 | GEO

Mediators in Crohn's disease influence the gene expression profiles of mesenchymal progenitor cells differentiated into the osteoblastic lineage.

Project description:Crohn's disease (CD) is associated with a higher prevalence of osteoporosis, a complication that is increasingly recognised as a significant cause of morbidity. Its pathogenesis is still controversial, but activity of CD is thought to be one contributing factor. Two-Color DRLL-IS-Design [Landgrebe et.al 2004: Efficient two-sample designs for microarray experiments with biological replications. In Silico Biology 4] including 12 Arrays, osteoporosis samples from 4 mc patients, control samples from 3 mc patients without osteoporosis

2012-03-16 | E-GEOD-20941 | biostudies-arrayexpress

Colonic Crohn's left and right colon

Project description:Colonic Crohn's Disease from a single patient in remission with mild disease index

2020-08-24 | GSE141553 | GEO

Differential early pathogenic changes in human ileal gene expression in Crohn's disease and ulcerative colitis

Project description:The aim of this study is to identify early pathogenic changes in ileal gene expression that precede the development of macroscopic disease in inflammatory bowel diseases (IBDs). We focused on two IBD phenotypes that were unlikely to overlap: 1) ileal Crohn‚Äôs disease (CD) patients undergoing initial ileocolic resection of diseased ileum; and 2) ulcerative colitis (UC) patients undergoing total colectomy. The Control patients were those patients without IBD undergoing initial right hemicolectomy or total colectomy. In order to identify early pathogenic changes in the human ileum in inflammatory bowel diseases, we analyzed 99 two-color whole human genome expression profiles (Agilent 4410A) of a test human ileal cRNA probe vs. a common reference human ileal RNA from a Control patient (N17). A minimum of four biopsies were taken from the macroscopically disease-unaffected proximal ileal margin of freshly resected specimens from 47 ileal Crohn's disease patients undergoing initial ileocolic resection, 27 ulcerative colitis patients undergoing total colectomy and 25 Control patients undergoing either right hemicolectomy or total colectomy. The test and common reference probes were synthesized using the Agilent Low Input Linear Amplification Kit. Hybridization was carried out in DNA hybridization chambers, washed and scanned on an Axon GenePix 4000B scanner. The preprocessing, filtering and normalization of the array data was carried out using the R package LIMMA.

2010-09-26 | E-GEOD-24287 | biostudies-arrayexpress

Fibrotic signatures in Crohn's disease patients

Project description:This study investigates the presence of specific fibrosis-associated gene expression signatures in Crohn's disease patient biopsies.

2022-01-02 | GSE192786 | GEO

Phagocyte-Associated Pathobionts in Crohn's Disease

Project description:This study evaluated lamina propria phagocyte gene expression and the associated microbiome in samples from Crohn's disease patients and controls.

2025-05-22 | GSE267465 | GEO

Transcriptomic analysis reveals the dynamic changes of immune responses during the development of creeping fat in Crohn's disease

Project description: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.

2023-09-06 | GSE227376 | GEO

RNA-seq of 4 Crohn's disease and 4 control

Project description:mRNA-seq raw data of 4 Crohn's disease and 4 control from colon tissue

2022-01-01 | GSE164871 | GEO

Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases

Project description:This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases. We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects.

2021-05-25 | GSE163314 | GEO

Human Blood Serum LC-MS/MS - Serological epithelial component proteins identify intestinal complications in Crohn's Disease

Project description:Quantitative proteome profiling was performed on Inflammatory (ICD), stricturing and fistulizing Crohn's Disease serums using label-free Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS).

2017-05-15 | PXD001821 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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