APOE genotype modifies the gene signature of microglial and astrocytic responses to aging

To determine how APOE genotypes impact the gene signature of microglia and astrocytes during aging at single cell level, we isolated brain cells from young (3 month of age) and aged (24 month of age) APOE2 and APOE3 and APOE4 mice, and conducted single cell RNA sequencing (scRNAseq) (4 mice/age/genotype). We annotated all the cells based on their gene markers and then focused on microglia and astrocytes for further downstream analysis. We functionally annotated each subcluster with microglia and astrocytes, based on the expression pattern of the widely accepted typical maker genes from multiple publications. Further, we identified the differentially expressed genes (DEG) in the comparison between young and aged mice for each subcluster in each APOE genotype and characterized the pathways related to these DEGs. Taken together, our dataset provided comprehensive resources to understand the APOE-regulated microglial and astrocytic responses to aging.