We used the single Col6a3 probeset (1424131_at_A). We selected the most representative probeset based on GeneNetwork quality scores for Ryr3 (1427427_at_A) and Klf12 (1455521_at; we also assessed the better of the two probesets showing Klf12 ethanol response (Wolen et al., 2012), 1439847_s_at). Robust multi-array average (RMA) normalized expression data were used for Spearman rank correlation analyses with ethanol behavioral phenotypes. Identifiers of probesets and phenotypes used for specific analyses are shown in Results and in Figure 5. Expression and phenotype data archived in GeneNetwork were produced in different labs and at different times; as a result, the N of BXD lines tested in our analyses varies across the tissues and phenotypes analyzed. We use the GeneNetwork default setting to retrieve the top 1000 correlations for each probeset × tissue pair.
