Four small populations of GABAergic interneurons were identified, including parvalbumin-expressing fast-spiking (FS), neuropeptide Y/somatostatin/nitric oxide synthase-expressing low-threshold-spiking (LTS), calretinin-expressing (CR), and cholecystokinin-expressing (CCK). A small cluster of cholinergic neurons was also identified (Ach). In addition to neurons, several glial cell populations were observed, including oligodendrocytes (the most prevalent cell type; 28.2% of the nuclei), oligodendrocyte progenitor cells (OPCs), astrocytes, ependymal cells, and microglia. Other cell types included non-microglial macrophages, endothelial cells, and vascular smooth muscle cells. Unexpectedly, glutamatergic neurons were found, although the caudate is known not to contain cell bodies of excitatory neurons. Their presence could reflect inadvertent inclusion of another brain region at the time of dissection; therefore, twenty samples that contained >10% of glutamatergic neurons were removed from all subsequent analyses (Supplementary Data 1 and 2), leaving 143 samples (74 with AUD, 69 without; 115 male, 28 female) with gene expression data for 1,121,762 nuclei, 250,537 of which also had ATAC data. Our cell type annotations correspond well to the cell groups from the recent Mammalian Basal Ganglia Consensus Cell Type Atlas released by Allen Institute34 (Supplementary Fig. 3).
