Array design and preparation of labeled cDNA and hybridizations to microarrays for the mouse liver and adipose tissue samples. RNA preparation and array hybridizations were again performed at Rosetta Inpharmatics. The custom ink-jet microarrays used in the BXH/wt, BXH/apoE, and BXC crosses were manufactured by Agilent Technologies. The array used for the BXH/apoE and BXH/wt samples consisted of 2,186 control probes and 23,574 noncontrol oligonucleotides extracted from mouse Unigene clusters and combined with RefSeq sequences and RIKEN full-length cDNA clones (Table S5). The array used for the BXC cross consisted of 39,280 noncontrol oligonuceotides again extracted from the mouse Unigene clusters and combined with RefSeq sequences and RIKEN full-length cDNA clones (Table S6).
