Fig. 3: M1- and M2-signature genes at single-cell resolution.

a Scheme of the in vitro differentiation of M1-type and M2-type macrophages. b Morphological changes during differentiation. c FACS analysis of the M1-specific marker CD80 and the M2-specific marker CD163 in differentiated M1 and M2 cells. The examined samples are colored with borders in a (black for monocytes, blue for M1 macrophages, and orange for M2 macrophages). d Unsupervised PCA primarily separated M1 and M2 macrophages by the first principal component. Cells are colored by cluster (upper) or sample origin (lower). e Gene expression levels of CD80 and CD163 in single-cell RNA-seq data confirmed M1 and M2 polarization. The thick black line indicates the median value of each sample. f M1-specific or M2-specific signature genes were extracted by overlapping differentially expressed genes from both donors. g Comparison with published gene sets derived from bulk M1 and M2 signatures²⁸. Only 29 genes were repeatedly extracted from single-cell and bulk signatures.