We performed deep RNA-seq experiments (>100 million reads per sample) from each of four brain regions (BLA, CE, NAC, SFC) from 60 individuals, 30 with and 30 without AUD (240 total samples). In addition, we obtained genotypes for all 60 subjects. After aligning RNA-seq reads to the human genome and imputing the SNP array genotyping to ~10 million SNPs, we retrieved allele counts from the RNA-seq data for all SNPs for which at least one sample was heterozygous, for a total of 250,007 SNPs. We focused on the ~17,000–24,000 SNPs in each of the four brain regions that had more than 10 reads in at least five heterozygous samples in both the AUD and control groups. The overall strategy is summarized in Supplementary Fig. 1 and Supplementary Table 1.
