part #900449) according to manufacturer's instructions, purified using the RNAeasy Mini Kit (Qiagen, Mountain View, CA), and quantified by absorbance at 260 nm. Labeled cRNA samples were hybridized to Mouse Genome 430 2.0 microarrays (Affymetrix, part #900497) according to the manufacturer's protocol and as described previously [21]. The number of microarrays involved in this study required that their processing be divided in batches of manageable sizes. To avoid systematic variation of expression data through technical batch effects, we performed a supervised randomization of samples into batch groups prior to each of the following processing stages: total RNA extraction, cRNA synthesis and hybridization. Both a saline and ethanol-treated mouse from a single strain were always processed together to minimize risk of technical variation confounding ethanol response detection. Annotation data for Mouse Genome 430 2.0 probe-sets was obtained from the GeneNetwork Data Sharing Zone (genenetwork.org/share/annotations).
