We performed peak calling on the aggregated ATAC-seq fragments from each cell type, thereby identifying cell type-specific open chromatin regions (see Supplementary Information). Chromatin accessibility showed a strong peak near the TSSs of several cell-type-specific genes (Supplementary Fig. 6a, b). We identified differentially accessible chromatin regions (DARs; open chromatin regions that differed in accessibility between individuals with and without AUD) for eight cell types (Supplementary Data 12). Only oligodendrocytes, astrocytes, D1 neurons, and D2 neurons had over 15 DARs (FDR < 0.05; Fig. 3a, b). Just as with the DEGs, most of the differences were in the positive direction; chromatin was on average more open in samples from individuals with AUD. However, most of these differences in chromatin accessibility were relatively small; only in oligodendrocytes did any DARs surpass an absolute log2 fold change of 0.5.
