Using data from the 143 samples, graph-based subclustering was performed for microglia, astrocytes, and D1 and D2 MSNs, the clusters that are known to have functional subtypes in the central nervous system35–37, and had a sufficient number of cells to analyze. There were four subclusters of microglia that roughly correspond to different activation states (Fig. 1b, Supplementary Data 3 and 4). Subcluster 1 (Resting Microglia) uniquely expressed genes specific to quiescent microglia, such as P2RY12 and CX3CR1, and was enriched for pathways relating to microglia migration. Subclusters 2 and 3 were both enriched for immune response-related genes, with subcluster 2 (Inflammatory Microglia) highly expressing genes involved in inflammation, such as TLR2. Subcluster 3 (CD83+ Microglia) was enriched for genes governing microglia activation, such as CD8338. Subcluster 4 (Phagocytosing Microglia), annotated by a recent cell type atlas as border-associated macrophages34 was marked by high expression of genes involved in endocytosis and phagocytosis. In individuals with at least 50 microglia cells, there was a significantly higher proportion of Inflammatory Microglia (subcluster 2) in individuals with AUD: 31%, versus 23% in those without
