Expression data from small intestine of NFKBIA-KO mice versus wild type

The IkB-Kinase (IKK)-NF-kB signaling pathway plays a multifaceted role in Inflammatory Bowel Disease: One the one hand it protects cells from apoptosis, but on the other, it activates transcription of numerous inflammatory cytokines and chemokines. To examine the role of constitutive NF-kB signaling in intestinal epithelium cells (IEC), we generated a mouse model with a tissue-specific knockout of the direct inhibitor of NF-kB, IkBα. We demonstrate that in IκBαIEC-KO mice, constitutive activation of NF-kB in epithelium leads to abnormal intestinal development, enlarged peyer’s patches, loss of Paneth cells, and spontaneous inflammation. We performed expression analysis of IκBαIEC-KO mice compared to wildtype by using the Affymetrix array Clariom S mouse. We utilized the Cre-loxP recombination system to generate a mouse line that allows tissue-selective deletion of IκBα. The targeting construct was designed in a way that Cre-mediated recombination results in deletion of the promoter region containing essential regulatory NF-κB binding sites, the core promoter, and the first two exons. To achieve tissue specific knockout, mice were crossed to Villin-Cre bearing mice. IκBαIEC-KO mice (Villin-Cre x floxed IκBα) were genotyped, depletion of IκBα was confirmed in each case by qRT-PCR on RNA extracted from bulk small intestine. Mice between 8-11 weeks of age were used for experiments. For each knockout mouse, a littermate sibling control was taken for comparison. For RNA extraction, duodenum was snap-frozen in liquid nitrogen and homogenized. RNA was extracted using Trizol reagent according to manufacturer’s instructions (Thermo Fisher). Preparation of cDNA, fragmentation and labeling was performed with the GeneChIPTM WT PLUS reagent kit (ThermoFisher Scientific). Samples were hybridized to the mouse Clariom™ S Assay (ThermoFisher Scientific).