In the same way as the RNA-seq data, pseudobulk chromatin accessibility data was created for the ATAC-seq data: For each cell type, the ATAC-seq counts matrices of each cell of that cell type were combined (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. See Supplementary Table 12 for a summary of the number of pseudobulk samples created for each cell type. 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.
