Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Bacterial physiology along the succession to DSS colitis

PROVIDER: PRJNA719860 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14146600_1.fastq.gz	Fastqsanger.gz
	SRR14146600_2.fastq.gz	Fastqsanger.gz
	SRR14146700_1.fastq.gz	Fastqsanger.gz
	SRR14146700_2.fastq.gz	Fastqsanger.gz
	SRR14146800_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1886

Similar Datasets

DSS Microbiota LC-MS/MS

Project description:In the DSS-induced colitis model, the epithelial damage and resulting inflammation is restricted to the colon, with a potential influence on the microbial composition in the adjacent cecum. Several studies have reported changes of the gut microbiota in the DSS-induced colitis model and other mouse models of IBD. Furthermore, metaproteomics analysis of the gut microbiome in a mouse model of Crohn’s disease demonstrated that disease severity and location are microbiota-dependent, with clear evidence for the causal role of bacterial dysbiosis in the development of chronic ileal inflammation. We have developed a refined model of chronic DSS-induced colitis that reflects typical symptoms of human IBD without a risky body weight loss usually observed in DSS models [Hoffmann et al., submitted]. In this study, we used metaproteomics to characterize the disease-related changes in bacterial protein abundance and function in the refined model of DSS-induced colitis. To assess the structural and functional changes, we applied 16S rRNA gene sequencing and metaproteomics analysis of the intestinal microbiota in three different entities of the intestinal environment, i.e. colon mucus, colon content and cecum content.

2020-03-17 | PXD007220 | Pride

Deciphering the combinatorial influence of diet and the microbiota on experimental colitis

Project description:Background & Aims: The complex interactions between diet and the microbiota that influence mucosal inflammation and inflammatory bowel disease are poorly understood. Experimental colitis models provide the opportunity to control and systematically perturb diet and the microbiota in parallel to quantify the contributions between multiple dietary ingredients and the microbiota on host physiology and colitis. Methods: To examine the interplay of diet and the gut microbiota on host health and colitis, we fed over 40 different diets with varied macronutrient sources and concentrations to specific pathogen free or germ free mice either in the context of healthy, unchallenged animals or dextran sodium sulfate colitis model. Results: Diet influenced physiology in both health and colitis across all models, with the concentration of protein and psyllium fiber having the most profound effects. Increasing dietary protein elevated gut microbial density and worsened DSS colitis severity. Depleting gut microbial density by using germ-free animals or antibiotics negated the effect of a high protein diet. Psyllium fiber influenced host physiology and attenuated colitis severity through microbiota-dependent and microbiota-independent mechanisms. Combinatorial perturbations to dietary protein and psyllium fiber in parallel explain most variation in gut microbial density, intestinal permeability, and DSS colitis severity, and changes in one ingredient can be offset by changes in the other. Conclusions: Our results demonstrate the importance of examining complex mixtures of nutrients to understand the role of diet in intestinal inflammation. Keywords: IBD; Diet; Microbiota; Mouse Models; Systems Biology

2017-10-30 | GSE104461 | GEO

H3K27me3 analysis in mouse colonic epithelial cells

Project description:H3K27me3 statuses were analyzed in normal mouse colonic epithelial cells and in those exposed to DSS-induced colitis, and aberrant changes of H3K27me3 by DSS-induced colitis were identified.

2015-10-15 | GSE74007 | GEO

Hematopoietic stem and progenitor cells integrate microbial signals to promote gut tissue repair

Project description:This study examines how bone marrow (BM)-resident hematopoietic stem and progenitor cells (HSPCs) are activated by bacterial insults for lineage specification to replenish the host hemato-immune system. We use the dextran sulfate sodium (DSS) colitis model to cause acute gut inflammation and observe molecular changes that occur in MPP2s, which expand both in the BM and MLN upon DSS treatment.

2022-07-07 | GSE207403 | GEO

mRNAs and miRNAs expression data from AOM/DSS, AOM, DSS and control mouse colon epithelial tissue at day100 when tumor formed in AOM/DSS bearing mice --- miRNA microarray

2013-05-10 | GSE44983 | GEO

Apple peel polyphenolic content as a key player for the prevention and treatment of experimental inflammatory bowel disease.

Project description:Colonic gene expression profiles of mice with DSS-induced colitis treated with apple peel polyphenolic extract Four-condition experiment: control, DSS-induced colitis, and mice treated with DAPP (two different doses (200 and 400 mg/kg/day) before or during induction and development of DSS-induced colitis.

2016-12-06 | GSE71920 | GEO

mRNAs and miRNAs expression data from AOM/DSS, AOM, DSS and control mouse colon epithelial tissue at day100 when tumor formed in AOM/DSS bearing mice --- miRNA microarray

Project description:To find out which miRNAs are significantly differential expression and potentially involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed miRNA microarray as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation. 5-7 weeks female BALB/c mice, (1) AOM/DSS group: AOM 12.5mg/kg i.p. at day 1, DSS drinking 5d/21dx3circles from day 5; (2) AOM group: AOM 10mg/kg i.p. 1/weekx6 from day 1; (3) DSS group: DSS drinking 5d/21dx3circles from day 5. The distal colon epithelial tissues were collected at day100 when tumor formed in AOM/DSS bearing mice. The miRNA microarray experiments were performed together.

2013-05-10 | E-GEOD-44983 | biostudies-arrayexpress

RNA-Seq from the colon tissues of DSS treated mice receiving either EP4-D, a selective E-type prostanoid receptor 4 agonist or vehicle

Project description:The experiment was designed to identify transcriptomic changes induced by selective EP4 agonism during experimental colitis. The mice received 1mg/ kg of the selective EP4 agonist, EP4-D or sterile phosphate buffered saline as vehicle control orally once per day concomitant with 3% DSS in drinking water. The DSS treatment was stopped on day 5 and mice were provided access to autoclaved drinking water for 3 additional days along with agonist and vehicle treatments once daily as described above. At the end of the treatment period, colon tissues from the mice were harvested, RNA isolated, and sequenced to identify transcriptional changes.

2021-02-01 | E-MTAB-9820 | biostudies-arrayexpress

Expression data from untreated and DSS-treated Adamts12 WT and KO mice

Project description:Adamts12-deficient mice undergo more severe colitis than WT mice after induction with DSS. We used microarrays to determine the gene expression differences between Adamts12-deficient and WT mice during ulcerative colitis induced with DSS (dextran sodium sulfate) Fragments of distal colon from DSS-treated (2% DSS during 7 days and 1 day of recovery) and untreated Adamts12-deficient and WT mice were obtained for RNA extraction and hybridiztion with Affymetrix microarrays

2012-09-01 | E-GEOD-40529 | biostudies-arrayexpress

Expression data from mouse colon tissue response to DSS induction at day 0, 2, 4 and 6

Project description:Temporal genome profiling of DSS colitis The DSS induced mouse colitis model is often used to emulate Ulcerative Colitis (UC) in order understand pathophysiological mechanism of inflammatory bowel disease (IBD). Given the progressive nature of IBD, colon tissue gene expression changes during the evolution of disease, and knowing the changes in gene expression profiles could indentify potential diagnostic markers or additional therapeutic targets for colitis. Therefore, we performed temporal genome expression profiling analysis using the Affymetrix genome wide microarray system to identify broad scale changes in gene expression associated with the development of colitis. Keywords: Expression time course of mouse colon tissue induced by 3% DSS. C57BL/6J mice were given 3% DSS in the drinking water and tissues from individual cohorts were collected at days 0, 2, 4 and 6. Total RNA were extracted from the colon tissue and detected by Affymerix GeneChip Mouse Genome 430 2.0 Array.

2010-10-13 | E-GEOD-22307 | biostudies-arrayexpress

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