Extended Data Fig. 1: Spatial transcriptomic DEGs examined by chromosome.

a, Heatmap colored by effect size from the spatial transcriptomic early-stage AD versus control differential gene expression analysis, with genes stratified by chromosome and by spatial region. Statistically significant (FDR < 0.05) genes with an absolute average log₂(fold change) ≥ 0.25 in at least one region are shown. b, Stacked bar chart showing the number of spatial transcriptomic early-stage AD control DEGs in each spatial cluster stratified by chromosome. c, Heatmap colored by effect size from the spatial transcriptomic late-stage AD versus control differential gene expression analysis, with genes stratified by chromosome and by spatial region. Statistically significant (FDR < 0.05) genes with an absolute average log₂(fold change) ≥ 0.25 in at least one region are shown. d, Stacked bar chart showing the number of spatial transcriptomic late-stage AD versus control DEGs in each spatial cluster stratified by chromosome. e, Spatial feature plots of four selected DEGs in one representative sample from each disease group.