Fig. 2. Mouse cerebellar nuclei cell types.

(A) Workflow of snRNAseq. The three regions were dissected separately, and cell nuclei were liberated, sorted for NeuN expression, and sequenced. (B) Marker expression for all neurons. Dashed line divides rhombic lip (RL)– and ventricular zone (VZ)-derived cells. N = 6 rounds of FACS using nine mice each. (C) Representative image of permanently labeled RL-derived cells probed for endogenous marker expression. Arrow, excitatory neuron; arrowhead, inhibitory neuron. Asterisk (*) in (B) and (C) labels Slc6a5+ RL-derived cluster e9*. Scale bar, 50 μm. N = 2 sections. (D and E) Clustering results for VZ- and RL-derived cells, labeled by clustering result (top) and CN dissection (middle), with marker expression at the bottom. Dissection labels are imperfect owing to close apposition of individual cerebellar nuclei in space. (F) Marker expression for all cell types. (G) Hierarchical clustering of excitatory cell types in the space of differentially expressed genes, using a correlation-based distance metric. Line color and gray numbers indicate bootstrapping-based branch confidence as in Fig. 1F. Class-A and Class-B neurons are color-coded with red and blue hues, respectively, in this and subsequent figures.