Extended Data Fig. 11: Gene signatures defining shared gradients in D1 and D2 medium spiny neurons.

(a) Constellation plot of clusters showing the pairs of similar clusters between 61 STR D1 Gaba and 62 STR D2 Gaba subclasses. Clusters are represented by a disk coloured by cluster, labelled by cluster ID, and disks with a coloured border are highlighted exemplars in panels b to f. (b-f) Representative MERFISH sections showing five examples of STR D1 and STR D2 cluster pairs from panel a, and their spatial distribution patterns. Sections are coloured by cluster identity. (g-h) Gene expression dot plots of two major gene modules driving the spatial gradient among STR D1 (g) and STR D2 (h) clusters. Dot size and colour indicate proportion of expressing cells and average expression level in each cluster, respectively. Underneath the dot plot, a violin plot of the medial-lateral coordinate for each MERFISH cell per cluster is shown. (i-p) Based on the gene modules (light blue and dark blue) identified in panels g-h, a cumulative gene score was calculated using UCell. UMAPs showing CNU-LGE GABAergic neurons (i,j,m,n), and representative MERFISH sections (k,l,o,p), coloured by the light blue gene module score for STR D1 (i,k) and STR D2 (j,l) types, or coloured by the dark blue gene module score for STR D1 (m,o) and STR D2 (n,p) types. Triangular schematic denotes the most granular hierarchical level shown in the panels (CL: cluster).