Eight cell types each contained over 700 differentially expressed genes (DEGs) (padj < 0.2) (Fig. 3A, Supplementary Table 7). We identified many changes in astrocytes, microglia, and in neurons, especially D1 and D2 medium spiny neurons. The magnitude of gene expression changes in neurons was generally smaller than in the astrocytes and microglia. In each of these cell types, more genes had higher expression in individuals with AUD than had lower. Many of the DEGs were differentially expressed in multiple cell types. Notably, astrocytes and oligodendrocytes had 833 DEGs in common, and D1 and D2 neurons had 538 DEGs in common (Extended Data Fig. 4). The differences in gene expression within D1 neurons and D2 neurons were highly correlated with each other (Pearson correlation = 0.83), while differences within other neuronal and non-neuronal cell types were more weakly correlated (Pearson correlation ranges = 0.10-0.46 for neuronal cell types and 0.05-0.27 for non-neuronal cell types; Fig. 3B, Supplementary Table 8). Interestingly, expression differences within D1/D2 neurons were much less correlated with either D1 or D2 neurons (r = 0.41 and 0.39 respectively).
