regions in each sample, and further scaled based on a trimmed mean of log transformed counts per million (CPM) value to correct for the variability of RNA composition in each sample (Robinson and Oshlack, 2010). The scaled CPM was used as gene level quantification in each sample. We used the edgeR package to identify the genes that are differentially expressed between alcohol drinking and water groups (Robinson et al., 2010). FDR was calculated according to Benjamini and Hochberg (1995). RPKM (Reads per Kilobase per Million Reads), which adjusts expression relative to transcript length, is reported in the tables and supplemental tables.
