Authors: Wei Yu Zhenwu Lin Danielle M Pastor John P Hegarty Xi Chen Ashley A Kelly Yunhua Wang Lisa S Poritz Walter A Koltun
Publish Date: 2010/02/18
Volume: 55, Issue: 11, Pages: 3171-3180
Abstract
Small interfering RNAmediated knockdown of Nkx23 in both cell lines was generated and highdensity cDNA microarrays representing over 25000 genes were performed Microarray results were validated by RTPCR and immunofluorescence Pathway analysis was used to identify gene networks associated with Nkx23 knockdown in these cell linesA total of 1677 genes were regulated by Nkx23 in CRS4 cells 1375 genes were regulated by Nkx23 in CRS61 cells Among those genes regulated by Nkx23 254 genes were similarly regulated by Nkx23 knockdown in both cell lines 159 genes were differentially regulated by Nkx23 knockdown between the two lines Genes regulated by Nkx23 were grouped primarily within the following two functional categories 1 immune and inflammatory response and 2 cell proliferation growth and oncogenesis Among the genes with similarly changed expression in the two cell lines the top affected pathways included antigen presentation and cell–cell signaling Among the genes with differentially changed expression between the two cell lines ingenuity pathway analysis indicated that the top affected pathway included genes directly involved in Wnt signalingGene expression profiling microarray experiments were performed at the Genomics Core of the Cleveland Clinic Lerner Research Institute contact PW Faber PhD faberpccforg We thank Dr Faber for his assistance with the cDNA microarray experiments This work was supported by a grant from the Philadelphia Health Care Trust WAK the Carlino Fund for IBD Research at the Penn State Milton S Hershey Medical Center College of Medicine WAK and through a Penn State Milton S Hershey Medical Center Department of Surgery Research Feasibility Grant ZL The authors have no financial disclosures
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