qRT-PCR was used to confirm microarray results. Genes that were previously identified by animal or human studies or related to stress or inflammatory response were selected for testing. Of the 22 genes selected for qRT-PCR on the basis of different expression after treatment with ethanol, 20 were confirmed with a p-value < 0.05, and one (FOXP1) had a similar fold and direction but with p=0.09 (Supplementary Table 5, Sections A & B). SRSF11, which was not confirmed, was measured on the array by 2 non-overlapping probe sets with different results, reflecting different splice variants; the differentially expressed variant contained a longer 3’ UTR which was not captured by the qRT-PCR. The eleven genes selected on the basis of differential expression between alcoholics and controls (8 overlapped with the set affected by ethanol) were confirmed with p< 0.05 (Supplementary Table 5, Sections B & C).
