For the liver microarray, clones were selected from a minimally redundant set of liver-derived EST and full-length cDNAs to create a minimally redundant set of clones. This was accomplished by screening them against the RefSeq database of known gene products. This set of clones was then fortified with cDNAs representing toxicologically relevant genes such as drug-metabolizing enzymes (e.g., cytochromes P450), inflammatory responsive genes (e.g., serum amyloid a1), and genes that we have previously identified as useful in classification of chemicals. All clones were then sequence verified from both 3' and 5' directions. These cDNAs were then amplified through PCR and purified using the Millipore Ultra-Screen system (Millipore Corporation, Billerica, MA). The cDNAs were then dried and resuspended in a 50/50 H2O/DMSO solution. Six replicates of each cDNA were printed on each array using a Microgrid II (Genomic Solutions, Ann Arbor, MA) at a pitch of 180 µm for a total of 27,648 features per chip. The slides were then baked at 80°C for 3 h and stored in a desiccator until their use.
