This April 2005 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 45 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 42 BXD recombinant inbred strains. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Samples were hybridized in small pools (n = 3) to a total of 105 Affymetrix M430A and B array pairs. This particular data set was processed using the RMA protocol. To simplify comparisons among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.