For the tissues that were processed at UTHSC (all BXD and LXS CNS tissues except HBP Affymetrix striatum), RNA was isolated using RNA STAT-60 (Tel-Test Inc., www.tel-test.com) as per manufacturer's instructions. Samples were then purified using standard sodium acetate methods prior to microarray hybridization. The eye samples required additional purification steps to remove eye pigment; this was done using the RNeasy MinElute Cleanup Kit (Qiagen, www.qiagen.com). RNA purity and concentration was evaluated with a spectrophotometer using 260/280 nm absorbance ratio, and RNA quality was checked using Agilent Bioanalyzer 2100 prior to hybridization. Array hybridizations were then done according to standard protocols.
