Microarray analysis

Total RNAs from the colon of three control and three HDAC1/2 IEC-specific knockout mice were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada). cDNA preparation and microarray assay were performed at the Microarray platform of the McGill University and Genome, Quebec Innovation Centre. An Affimetrix GeneChip mouse genome 430 2.0 array, displaying over 34,000 murine gene sequences, was used for hybridization. Data analysis, normalization average difference and expression measurements were subsequently completed with Flexarray software version 1.6.1. Background correction and normalization were assessed with a multi-array average (RMA) algorithm. Significant statistical differences were calculated with Welch’s t test, with the cut-off for statistical significance set to a p value below 0.05. Classification of genes according to their Gene Ontology biological processes was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) v 6.7 (http://david.abcc.ncifcrf.gov/) [26] and the ToppGene suite for functional gene enrichment analysis and candidate gene priorization (http://toppgene.cchmc.org/) [27]. Both analysis tools gave similar results regarding biological processes, and the highest gene count and lowest p value were selected. Microarray data have been deposited in the Gene Expression Omnibus database (GSE47745).