Investigation Title Human colon expression in healthy controls and UC Comment[Submitted Name] Human colon expression in healthy controls and UC Experimental Design transcription profiling by array Experimental Design Term Source REF EFO Comment[SecondaryAccession] GSE10191 Comment[ArrayExpressReleaseDate] 2010-05-15 Comment[AEMIAMESCORE] 2 Comment[ArrayExpressAccession] E-GEOD-10191 Comment[MAGETAB TimeStamp_Version] 2010-07-29 18:01:28 Last Changed Rev: 13058 Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Person Last Name Denson Person First Name Lee Person Mid Initials Person Email lee.denson@cchmc.org Person Phone Person Fax Person Address CCHMC, 3333 Burnet Avenue, Cincinnati, USA Person Affiliation CCHMC Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2010-05-15 PubMed ID 18981162 Publication DOI 18981162 Publication Author List 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 Publication Title Intestinal macrophage/epithelial cell-derived CCL11/eotaxin-1 mediates eosinophil recruitment and function in pediatric ulcerative colitis. Publication Status journal_article Publication Status Term Source REF The MGED Ontology Experiment 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. Protocol Name P-GSE10191-2 P-GSE10191-3 P-GSE10191-4 P-GSE10191-5 P-GSE10191-6 P-GSE10191-1 Protocol Type nucleic_acid_extraction labeling hybridization image_aquisition feature_extraction bioassay_data_transformation Protocol Description RNeasy Plus Mini kit (QIAGEN, Hilden, Germany) Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA amplified with TargetAmp 1-round Aminoallyl-aRNA Amplication Kit 101 (Epicentre, WI) (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the human HG-U133 Plus 2.0 GeneChip array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the Affymetrix Genechip Scanner 3000. The data were analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Hs133P_Hs_REFSEQ_8) , then normalized to the internal control for each batch and the mean of the healthy control reference samples. ID_REF =
VALUE = data was RMA normalized, then normalized to the internal control sample for each batch and the mean of the healthy control reference samples Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF The MGED Ontology The MGED Ontology SDRF File E-GEOD-10191.sdrf.txt Term Source Name The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version