Twelve biological replicate samples per treatment group were utilized for analysis. Gene expression array analysis was performed using the Applied Biosystems 1700 Gene Expression Array System (Foster City, CA). The ABI rat genome survey microarray contains probes representing a complete, annotated, and manually curated set of approximately 27,000 rat genes from both the public and Celera databases. Analysis was performed according to the manufacturer’s protocol using the Functional Genomics Core Laboratory at The University of Chicago, under the direction of Dr. Xinman Li. Briefly, Digoxigenin-UTP-labeled cRNA was generated and linearly amplified from 2 μg of total RNA using the ABI chemiluminescent RT-IVT labeling kit. Arrays were prehybridized for 1 hour at 55°C in hybridization buffer with blocking reagent. Ten μg of labeled cRNA was incubated in fragmentation buffer for 30 minutes at 60° and subsequently hybridized to each microarray in 0.5 ml hybridization buffer for 16 hours. Chemiluminescent detection and image acquisition were performed using the ABI chemiluminescence detection kit and 1700-microarray analyzer. Primary image analysis was performed using the ABI microarray analyzer software package.
