Single-end indexed nanowell sciATAC produces high-coverage profiles. (A) Single-end indexed adapter design for nanowell sciATACv3. (B) UMAP of 21,239 mouse brain chromatin accessibility profiles produced using nanowell sciATACv3. Dashed line indicates interneuron cell clusters. (C) Cell type module scoring for clusters in panel A. (D) Marker gene tracks for clusters. (E) Integration of GABAergic neurons with scRNA-seq neurons from mouse isocortex and hippocampus. As expected, some clusters are present in whole brain data (ATAC, red) that are not in the RNA data set (blue). (F) Label transfer of scRNA cell types used to guide cell type identification. Unmatched clusters were typed using gene set module scores and marker gene profiles.
