Extended Data Fig. 6: Additional gene expression and spatial analysis of astrocytes.
a, Spatial map of astrocyte subtypes in control and TauPS2APP samples. Scale bars, 100 µm. b, Cell-type composition around Aβ plaque in different distance intervals for the TauPS2APP samples at eight months. Stacked bar plot showing the density of each astrocyte subpopulation in each distance interval around the Aβ plaque. The overall cell density of each subpopulation in each region was included as the reference for comparison. Asterisks denote significantly enriched astrocyte subclusters in each distance interval. One-sided one-sample t-test, *P < 0.05, **P < 0.01 vs. overall cell density. c, Volcano plots showing the differentially expressed genes of astrocytes in AD and control comparison at eight and 13 months (y-axis: -log adjusted p-value, x-axis: average log fold change). The two-sided Wilcoxon rank-sum test. Genes (p-value < 0.05, absolute value of lnFC > 0.1) are marked in red (up-regulated) or blue (down-regulated). d, Gene ontology enrichment analysis (Fisher’s one-sided test) results of DEGs in astrocytes of the 13-month TauPS2APP samples. e, Matrix plot showing the z-scores of SDEGs of microglia across multiple distance intervals from plaques. f, Barplots showing the DEG enrichment significance (the Chi squared test) of co-expression modules of astrocyte identified by scWGCNA. The gene module with the most significant DEG enrichment (AM3) is highlighted. g, Matrix plot showing the averaged z-score value of astrocyte gene modules across multiple distance intervals.
