Extended Data Fig. 9: TCR-, cytokine- and TCR+cytokine-stimulated MAIT cells.

a,b, UMAPs of 20 h- (a) and 68 h- (b) stimulated MAIT cells split and colored by donor. c, UMAPs of 20 h-stimulated MAIT cells colored by expression of IFNG, IL26, CCL3 and TNFRSF9. d, UMAP of 20 h-stimulated MAIT cells colored by expression of 4-1BB protein. e, UMAP of 20 h-stimulated MAIT cells colored by expression of GZMB. f, Pearson’s correlation between the log₂ fold change in protein expression between TCR-stimulated and unstimulated MAIT cells, and TCR+cytokine-stimulated and unstimulated MAIT cells. Labels highlight selected genes that were differentially regulated by the two stimuli. Point colors indicate whether the protein was significantly differentially expressed in response to TCR stimulation only (orange), TCR+cytokine stimulation only (maroon), both (black) or neither (NS; gray). g, Pearson’s correlation between the log₂ fold change in protein expression between cytokine-stimulated and unstimulated MAIT cells, and TCR+cytokine-stimulated and unstimulated MAIT cells. Labels highlight selected genes that were differentially regulated by the two stimuli. Point colors indicate whether the protein was significantly differentially expressed in response to cytokine stimulation only (purple), TCR+cytokine stimulation only (maroon), both (black) or neither (NS; gray). h, UMAP of 20 h-stimulated MAIT cells colored by the 13 identified clusters. i, Dot plot showing the top three marker genes per cluster in h. Red box indicates the IL-17-expressing cluster. Dot color indicates the level of gene expression and dot size indicates the percentage of cells expressing the gene. j, UMAP of 68 h-stimulated MAIT cells colored by the nine identified clusters. k, Dot plot showing the top three marker genes per cluster in j. Red box indicates the IL-17-expressing cluster. Dot color indicates the level of gene expression and dot size indicates the percentage of cells expressing the gene.