For the 267,100 cells in which both gene expression and chromatin accessibility data were available (see Extended Data Fig. 5 for cell type distribution for snATAC-seq cells), the chromatin accessibility (combined reads for each cell type) showed a strong signal near the transcription start sites (TSS) of its respective marker genes of several cell type-specific genes (Extended Data Fig. 6). Thirty-six percent of all open chromatin regions were shared among neuronal and non-neuronal cell types, while 34% of the peaks were unique to neurons and 30% unique to non-neurons (Fig. 4A). D1 neurons and D2 neurons had very similar open chromatin regions (Jaccard index = 0.8) and were less similar to D1/D2 neurons (Jaccard index = 0.47). Astrocytes, oligodendrocytes, and OPCs had moderately similar open chromatin regions, with Jaccard indices of approximately 0.4 between these cell types (Fig. 4B, Supplementary Table 10).
