Samples from 9 different regions of the brains of each of 4 individuals (2 male and 2 female; an alcoholic and a control of each sex) were obtained from the NIAAA-supported brain bank at the Tissue Resource Center located in the Neuropathology Unit of the Department of Pathology, University of Sydney, Australia. We extracted total RNA from each of the nine regions of each individual brain: prefrontal cortex, cerebral cortex, thalamus, visual cortex, hippocampus, amygdala, caudate nucleus, putamen and cerebellum. RNA was extracted using Trizol (Invitrogen), with a higher ratio of Trizol to tissue to improve yield and purity (Edenberg et al., 2005), and further purified using RNeasy mini-columns (Qiagen, Valencia, CA). Samples were labeled using the Affymetrix Whole-Transcript labeling protocol starting with 100 ng of total RNA. The labeled samples were hybridized to Human Gene 1.0 ST arrays, then washed, stained and scanned as described above.
