In the same way as the RNA-seq data, pseudobulk chromatin accessibility data were created for the ATAC-seq data: For each cell type, the ATAC-seq count matrices of each cell of that cell type were summed by sample ID, for the 143 samples. Samples were removed on a cell type-specific basis if the sample contained less than 50 cells of that cell type (Supplementary Data 12). Due to a low number of samples meeting the ≥50 cell criteria, differential accessibility analysis was not performed for cholinergic interneurons, vSMCs, CCK interneurons, macrophages, ependymal cells, LTS interneurons, or endothelial cells. Supplementary Figs. 12 and 13 display samples plotted by the top two principal components of pseudobulk-level counts for each cell type, separated by AUD classification and sex.
