By rRNA depletion RNA-seq analysis of the 192 selected Set 1 samples (from 8 brain regions), we identified 97 differentially expressed (absolute FC > 2.0 & P < 0.001) coding genes (or mRNAs) in one or more brain regions (5 in AMY, 4 in CN, 21 in CRB, 11 in HIP, 4 in NAc, 46 in PFC, 11 in PUT, and 6 in VTA) of AUD subjects (Fig. 2 and Table S5). Three coding genes were upregulated (>2-fold increase & P < 0.001) in multiple brain regions (CHI3L1: AMY, PUT, and VTA; FSIP2: CN, NAc, PFC, and PUT; and MAFB: CRB and VTA) of AUD subjects, while two other coding genes were downregulated (>2-fold decrease & P < 0.001) in multiple brain regions (CYYR1: CN, CRB, and HIP; EDN3: CN, HIP, NAc, and PUT) of AUD subjects.
