Female h-NAG-1 transgenic mice and wild type C57BL/6J mice at 5 weeks of age were placed on either 10% fat diet (D12450B) or 60% fat diet (D12492, Research Diets, New Brunswick, NJ) for 20 weeks.
Total RNA in colon epithelium was prepared using AllPrep DNA/RNA Mini Kit (Qiagen).
Starting with 500ng of total RNA, Cy3-labeled cRNA was produced according to Agilent's protocol.
For each sample, 1.65ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.
Slides were washed and then scanned with an Agilent Scanner.
The feature extractor processed signal intensity values were log2 transformed, quantile normalized, the multiple values for same probe were summarized using median polish. The resulting value was batch corrected using Emprical Bayes method from Johnson et al. 2006 (Johnson EW, Rabinovic A, Li C . Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics Advance Access published on April 21, 2006, DOI 10.1093/biostatistics/kxj037).