In this study, we sequenced and annotated more than 12,000 clones from the same cDNA library and fabricated a microarray for the non-redundant clones. The primary purpose was to identify and characterize gene expression profiles in six brain regions, namely the amygdala, hippocampus, NA, prefrontal cortex (PFC), striatum, and ventral tegmental area (VTA), of Sprague-Dawley rats in response to chronic nicotine treatment.