Samples from the caudate nucleus of post-mortem brains from the New South Wales Brain Tissue Resource Centre at the University of Sydney were sequenced in the sn-multiome assay, in which transcription levels and chromatin accessibility were measured in the same nuclei; most were also sequenced using the 10X HT snRNA-seq assay. After demultiplexing and data processing, samples with <200 cell barcodes were removed, leaving 163 samples, 82 with and 81 without AUD; 128 male and 34 female. Low quality nuclei were filtered out from further analyses based on number of genes, number of molecules, and percentage of mitochondrial DNA (see “Initial quality control” in “Methods”), leaving gene expression levels for 1,307,323 nuclei and chromatin accessibility (ATAC-seq) for 267,100 of these nuclei (Demographics are in Supplementary Data 1 and 2, and detailed experimental procedures are in “Methods”). Graph-based clustering of the snRNA-seq data of the 163 samples identified 17 distinct cell clusters (Fig. 1a, Supplementary Fig. 2a). There was no significant difference in relative abundance of cell types between samples from individuals with and without AUD (Supplementary Fig. 2b; see “Methods”).
