Extended Data Fig. 4: Summary of scRNA-seq data, selected identity gene expression and gene ontology of significantly enriched genes.

a, UMAP visualization of the cell-type composition of the PiChip cultures by single-cell transcriptome profiles. Distinct cell types are depicted with different colors. b, Dot plot of identity genes for distinct cell types. Color scale (a.u.) indicates the average of expression of identity genes in each cell population, and dot size is proportional to the percentage of cells expressing the identity genes. c, Number of significantly upregulated (FDR < 0.2 and FC > 0) and downregulated (FDR < 0.2 and FC < 0) genes across distinct cell types. Significantly upregulated genes are depicted in red, while downregulated are in blue. d, Volcano plots of differentially expressed genes in all cell types in AD cultures versus CTRL. Significantly upregulated (P < 0.05 and FC > 0.1) and downregulated (P < 0.05 and FC < 0.1) genes are shown in red and blue dots, respectively (P-values from Wilcoxon Rank Sum test). e, Gene ontology of significantly upregulated pathways in all cell types in AD versus CTRL. From left to right, the order of conditions is the same as in d. Color scale indicates the adjusted P-value for significantly enriched pathways in each cell population. f, Gene ontology/network analysis of significantly upregulated genes (P < 0.05 and FC > 0.1). Top five category was visualized for associated genes and pathways. g, Gene ontology of significantly downregulated pathways in all cell types in AD versus CTRL. From left to right, the order of conditions is the same as in d. Color scale indicates the adjusted P-value for significantly enriched pathways in each cell population. h, Gene ontology/network analysis of significantly downregulated genes (P < 0.05 and FC < 0.1). Top five category was visualized for associated genes and pathways (e-h, P-values were calculated from a Fisher exact test and the adjusted p-values given by Benjamini & Hochberg method).