E-GEOD-10191 - Human colon expression in healthy controls and UC

Status
Submitted on 16 January 2008, released on 15 May 2010, last updated on 27 March 2012
Organism
Homo sapiens
Samples (23)
Array (1)
Protocols (6)
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.
Experiment type
transcription profiling by array 
Contact
Citation
Intestinal macrophage/epithelial cell-derived CCL11/eotaxin-1 mediates eosinophil recruitment and function in pediatric ulcerative colitis. Ahrens R, Waddell A, Seidu L, Blanchard C, Carey R, Forbes E, Lampinen M, Wilson T, Cohen E, Stringer K, Ballard E, Munitz A, Xu H, Lee N, Lee JJ, Rothenberg ME, Denson L, Hogan SP.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-10191.idf.txt
Sample and data relationshipE-GEOD-10191.sdrf.txt
Raw data (1)E-GEOD-10191.raw.1.zip
Processed data (1)E-GEOD-10191.processed.1.zip
Experiment designE-GEOD-10191.biosamples.png, E-GEOD-10191.biosamples.svg
Array designA-GEOD-5760.adf.txt
R ExpressionSetE-GEOD-10191.eSet.r
Links