SNr neurons were identified with a similar procedure (SN/VTA dataset). Of 4 global neuron clusters (Figure 6F), one (cluster 3, n=10,049 cells) contained SNr neurons (Figure 6G). Other clusters contained hippocampal (cluster 1, n=73 cells), thalamic (cluster 2, n=297), and dopaminergic (cluster 4, n=1,841) populations. Within cluster 3, 6 of the 19 subclusters mapped to the SNr (Figure 6H–J and Figure S6E–H). Two subcluster pairs shared selective markers (3–18/3–19: Sema3a, Adarb2; 3–17/3–13: Pax5, Pou6f2), suggesting relatedness, but were distinguished by ion channels (Kcnc3, Kcna1), transmembrane proteins (Tmem132c), and transcription factors (Pou3f1) that could imply a state or subtype distinction (Figure 6I). Of the remaining subclusters, 3–12 expressed Slc17a6±, likely corresponding to the glutamatergic projection to thalamus (Antal et al., 2014). Subcluster 3–2 was Gad2+/Pvalb− and expressed the developmental marker Zfpm2 (Lahti et al., 2016), likely representing a third GABAergic type marked by Sox14 and Cplx3 expression (Figure 6I).
