Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-9686 - Human colon expression in healthy, CD, treated CD, and UC

Status
Submitted on 26 November 2007, released on 27 May 2010, last updated on 27 March 2012
Organism
Homo sapiens
Samples (33)
Array (1)
Protocols (7)
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.
Experiment type
unknown experiment type 
Contact
Citation
Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease. Carey R, Jurickova I, Ballard E, Bonkowski E, Han X, Xu H, Denson LA.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-9686.idf.txt
Sample and data relationshipE-GEOD-9686.sdrf.txt
Raw data (1)E-GEOD-9686.raw.1.zip
Processed data (1)E-GEOD-9686.processed.1.zip
Array designA-GEOD-5760.adf.txt
R ExpressionSetE-GEOD-9686.eSet.r
Links