Figure 3.

Single cell and nucleus RNA sequencing of human CNS tissues indicates that both fresh and frozen nuclear transcriptomes closely approximate and reflect microglia gene expression heterogeneity. (a) PCA plot of fresh‐tissue derived cells and nuclei, and nuclei isolated from adjacent frozen tissue samples. (b) UMAP plot depicting five clusters identified in the merged single cell and nucleus transcriptomes of microglia from two human donors. (c) UMAP plot where colors indicate the different experimental samples, fresh tissue‐derived microglia cells and fresh and frozen tissue‐derived nuclei. (d) UMAP plot depicting expression (log‐transformed UMI counts per 10,000 transcripts) of canonical microglial genes C1AQ, P2RY12, and CD74. (e) The proportion of clusters across the indicated experimental samples