sciATACv2 on whole mouse brain. (A) UMAP of 224,986 cells colored by cluster and annotated for cell type class. (B) Integration with mouse isocortex and hippocampus scRNA-seq neuron-enriched data. As expected, the whole mouse brain ATAC data set (red) includes cell populations not present in the RNA data set (blue), predominantly for non-neuronal cell types which were depleted in the RNA data set. (C) Label transfer of scRNA cell type classes on the integrated UMAP, and shown on the ATAC UMAP (D). (E) Gene module scores used to confirm RNA assignments and annotate clusters present only in the ATAC data. (F) Marker gene tracks used as the final confirmation of cell type assignment.
