Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mouse colon expression in wild type and STAT5b deficient mice

ABSTRACT: Regulation of epithelial barrier function is dependent upon precise control of cell survival and activation of inflammatory pathways in response to the enteric flora. These experiments tested differential colon gene expression relative to these pathways in wild type and STAT5b deficient mice. Keywords: Single time point in wild type and STAT5b deficient mice. Colon RNA was isolated from adult wild type and STAT5b deficient mice.

ORGANISM(S): Mus musculus

SUBMITTER: Xiaonan Han

PROVIDER: E-GEOD-8942 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Regulation of intestinal barrier function by signal transducer and activator of transcription 5b.

Han X X Ren X X Jurickova I I Groschwitz K K Pasternak B A BA Xu H H Wilson T A TA Hogan S P SP Denson L A LA

Gut 20080807 1

<h4>Background</h4>Colon epithelial cell (CEC) apoptosis and nuclear factor-kappaB (NF-kappaB) activation may compromise barrier function, and it has been reported that signal transducer and activator of transcription 5b (STAT5b)-deficient mice exhibit increased susceptibility to colitis. It is hypothesised that the growth hormone (GH) target STAT5b maintains mucosal barrier integrity by promoting CEC survival and inhibiting NF-kappaB activation.<h4>Methods</h4>The GH effect upon mucosal injury ...[more]

PMID: 18687707

Similar Datasets

Transcription profiling of mouse rectum after physiological stress

Project description:Using isolation stress model, we showed that goblet cell-dependent mucosal barrier functions in the mouse rectum was more vulnerable to stress than the colon. We also found that isolation stress specifically stimulated IL-18 production only in the rectum. Furthermore, the crucial role of IL-18 in the stress response of the mouse rectum was confirmed using IL-18 knockout mice. Microarray analysis was used to assess the stress response and to identify responsible genes for the vulnerability of the mouse rectum to isolation stress. Experiment Overall Design: Total RNA was prepared from the colon and the rectum of wild-type and IL-18 knockout mice before isolation and 8 days after starting isolation. The one GSM sample of microarray analysis was made by pooling an equal amount of total RNA 5 mice of each group. Agilent whole mouse genome oligonucleotide microarray was used to measure gene expression in these samples according to the manufactureâ??s protocol.

2009-02-26 | E-GEOD-11910 | biostudies-arrayexpress

Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UC

Project description:Colon gene expression in human IBD. The three major clinical subsets of Inflammatory Bowel Disease (IBD) include colon-only Crohn's Disease (CD), ileo-colonic CD, and Ulcerative Colitis (UC). These experiments tested differential colon gene expression in these three types of IBD, relative to healthy control samples, and the local degree of mucosal inflammation as measured by the CD Histological Index of Severity (CDHIS). Colon biopsy samples were obtained from IBD patients at diagnosis and during therapy, and healthy controls. The global pattern of gene expression was determined using GeneSpring software, with a focus upon candidate genes identified in a recent genome wide association study in pediatric onset IBD. Data suggested that two of these candidate genes are up regulated in pediatric IBD, partially influenced by local mucosal inflammation. These experiments tested differential colon gene expression in healthy, CD, and UC samples for candidate genes identified in a recent pediatric onset IBD genome wide association study. Keywords: Single time point in CD and UC and healthy controls. Colon RNA was isolated from biopsies obtained from CD and UC at diagnosis and during therapy and healthy controls. Samples were obtained from the most proximal affected segment of colon. Microarray experiments were performed as described in the CCHMC microarray core, and data was analyzed as described above in the summary. The '107' internal control CEL files (for batches 1,2,3,4,5) used for normalization of the Sample VALUEs are also contained within this data set.

2009-03-10 | E-GEOD-10616 | biostudies-arrayexpress

Human colon expression in healthy controls and UC

Project description:Activation of inflammatory pathways in human IBD. Leukocyte recruitment pathways including those for eosiniphils are activated in the affected colon in IBD. However, the functional implications of this are not known. We hypothesized that pro-inflammatory eotaxin (CCL11) dependent networks would be up regulated in the colon of pediatric patients with Ulcerative Colitis (UC), and that these would regulate eosinophil recruitment to the gut. These experiments tested differential colon gene expression relative to these pathways in healthy and UC samples. Colon biopsy samples were obtained from UC patients at diagnosis, and healthy controls. The global pattern of gene expression was determined using GeneSpring software, and biological networks were identified using Ingenuity software. Data suggested that a leukocyte recruitment network which includeds CCL11 is up regulated in pediatric UC at diagnosis. The degree of up regulation of these genes compared to healthy controls was remarkably conserved within the UC patient group, suggesting common mechanisms of mucosal inflammation. These experiments tested differential colon gene expression relative to these pathways in healthy and UC samples. Keywords: Single time point in UC and healthy controls. Colon RNA was isolated from biopsies obtained from UC at diagnosis and healthy controls. Samples were obtained from the most proximal affected segment of colon. Microarray experiments were performed as described in the CCHMC microarray core, and data was analyzed as described above in the summary. The '107' internal control CEL files (for batches 1,2,4,5) used for ormalization of the Sample VALUEs are also contained within this data set.

2010-05-15 | E-GEOD-10191 | biostudies-arrayexpress

Mouse colon expression in wild type and STAT5b deficient mice

Project description:Regulation of epithelial barrier function is dependent upon precise control of cell survival and activation of inflammatory pathways in response to the enteric flora. These experiments tested differential colon gene expression relative to these pathways in wild type and STAT5b deficient mice. Keywords: Single time point in wild type and STAT5b deficient mice.

2008-08-15 | GSE8942 | GEO

Loss of colonic primary cilia promotes inflammation and carcinogenesis

Project description:Primary cilia (PC) are important signaling hubs in cells and we explored their role in colorectal cancer (CRC) and colitis. In the colon we found PC to be mostly present on different subtypes of fibroblasts and exposure of mice to either chemically induced colitis-associated colon carcinogenesis (CAC) or dextran sodium sulfate (DSS)-induced acute colitis decreased PC numbers. We employed conditional knock-out strains for the PC essential genes, Kif3A and Ift88, to generate mice with reduced numbers of PC on colonic fibroblasts. These mice showed an increased susceptibility in the CAC model as well as in DSS-induced colitis. Secretome and immunohistochemical analyses of DSS-treated mice displayed an elevated production of the pro-inflammatory cytokine IL-6 in PC-deficient colons. An inflammatory environment diminished PC presence in primary fibroblast cultures. This was triggered by IL-6 as identified by RNAseq analysis together with blocking experiments, suggesting an activation loop between IL-6 production and PC loss. Notably, an analysis of PC presence on biopsies of patients with ulcerative colitis as well as CRC patients revealed decreased numbers of PC on colonic fibroblasts in pathological versus surrounding normal tissue. Taken together, we provide evidence that a decrease in colonic PC numbers promotes colitis and CRC.

2022-11-29 | PXD033440 | Pride

Human colon expression in healthy, CD, treated CD, and UC

Project description:Activation of inflammatory pathways in human IBD IL-6:STAT3 pathways are activated in the affected colon in IBD. However, the functional implications of this are not known. We hypothesized that pro-inflammatory IL-6:STAT3 dependent networks would be up regulated in the colon of pediatric patients with Crohn Disease (CD) and Ulcerative Colitis (UC), and that these would regulate leukocyte survival, proliferation, and recruitment to the gut. These experiments tested differential colon gene expression relative to these pathways in healthy, CD, and UC samples. Colon biopsy samples were obtained from CD and UC patients at diagnosis, CD patients during therapy, and healthy controls. The global pattern of gene expression was determined using GeneSpring software, and biological networks were identified using Ingenuity software. Data suggested that two IL-6:STAT3 dependent networks are up regulated in pediatric IBD both at diagnosis and during therapy which regulate leukocyte recruitment and survival. The degree of up regulation of these genes compared to healthy controls was remarkably conserved across the two CD groups and the UC groups, suggesting common mechanisms of mucosal inflammation. Colon RNA was isolated from biopsies obtained from CD at diagnosis and during therapy, UC at diagnosis, and healthy controls. Samples were obtained from the most proximal affected segment of colon. Microarray experiments were performed as described in the CCHMC microarray core, and data was analyzed as described above in the summary. The '107' internal control CEL files (for batches 1-4) used for normalization of the Sample VALUEs are linked below as supplementary files.

2010-05-27 | E-GEOD-9686 | biostudies-arrayexpress

Mus musculus

Project description:Mouse colon expression in wild type and STAT5b deficient mice

| PRJNA102365 | ENA

Gene expression analysis of human adenomas.

Project description:Gene expression profiling was carried out in 7 matched colon adenoma samples and normal mucosa to characterize the molecular mechanisms relevant to the etiology ofadenoma and human colorectal carcinoma development. Whole-transcriptome RNA sequencing of the 7 matched colon adenoma samples and normal mucosas.

2016-09-08 | E-GEOD-72820 | biostudies-arrayexpress

Regulation of Mouse Lens Development and Gene Expression by KrÃ¼ppel-Like Factor 4

Project description:Conditional disruption of Klf4 in the ectoderm-derived tissues of the eye results in defective cornea, conjunctiva and the lens. Expression of Klf4 is first detected in the embryonic day-12 (E12) mouse lens, peaks at E16, and declines thereafter. Lenses from Mice which were conditional null for Klf4 (Klf4CN) were characterized by morphology and transcriptome. Wild type and Klf4-conditional null mouse lens gene expression at embryonic day 16.5 (E16.5) and postnatal day 56 (PN56) was surveyed using Affymetrix mouse whole genome 430 2 arrays.

2013-07-01 | E-GEOD-47694 | biostudies-arrayexpress

Quantitative proteogenomic characterization of inflamed murine colon tissue using an integrated discovery, verification, and validation proteogenomic workflow

Project description:Rag2-/-Il10-/- mice were subjected to infection by Helicobacter hepaticus and allowed to develop long-term infections. Proximal colon tissue was then harvested from the mice for analysis. RNA was isolated from the samples and submitted for transcriptomic analysis; this data was then used to create a custom RNA-based FASTA database. Protein isolated from the proximal colon samples were digested and analyzed via bottom-up mass spectrometry. The custom FASTA database was then used for proteogenomic analysis of the raw mass spectrometry data in the Galaxy for proteomics (Galaxy-P) platform.

2022-05-19 | PXD028407 | Pride

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