Extended Data Fig. 4. Alignment of EC and SFG maps homologous excitatory neuron subpopulations.

a, tSNE projection of excitatory neurons from the EC and SFG in the joint alignment space, colored by subpopulation identity (top), individual of origin (middle), or brain region (bottom). b, Heatmap and hierarchical clustering of subpopulations and subpopulation marker expression (top subpanel); “High” and “Low” relative expression reflect above- and below-average expression, respectively (see Methods). Relative abundance of subpopulations across Braak stages (second and third subpanels); for each brain region, statistical significance of differences in relative abundance across Braak stages (Braak 0 n=3, Braak 2 n=4, Braak 6 n=3, where n is the number of individuals sampled) was determined by beta regression and adjusted for multiple comparisons (see Methods). Expression heatmap of EC layer-specific genes identified from Ramsden et al.²² (fourth subpanel). Expression heatmap of neocortical layer-specific genes from Lake et al.¹² (fifth subpanel). Expression of selectively vulnerable EC excitatory neuron subpopulation markers by excitatory neurons in the EC (sixth subpanel) or SFG (bottom subpanel). Significant beta regression P values (adjusted for multiple testing) are shown in a table at the bottom of the panel. c, Sankey diagram connecting subpopulation identity of excitatory neurons in the EC alignment space and the SFG alignment space to subpopulation identity in the EC+SFG alignment space. The links connecting EC:Exc.s2 and EC:Exc.s4 to SFG:Exc.s2 and SFG:Exc.s4, respectively, are highlighted.