Figure 4: Treg-committed Th17 cells differentiate in the absence of Foxp3.

A) UMAP of scRNA-seq data showing PhenoGraph clusters of tdTomato⁺GFP⁺ reporter-null cells and tdTomato⁻GFP⁻ bulk CD4 T cells isolated from the colonic lamina propria of three female Foxp3^{ΔEGFPiCre/wt}R26^{lsl-tdTomato/wt} mice. B) Expression of select marker genes by cells occupying distinct PhenoGraph clusters. C-D) UMAP and PhenoGraph cluster composition of scRNA-seq data for individual replicates of tdTomato⁺GFP⁺ reporter-null cells and tdTomato⁻GFP⁻ bulk CD4 T cells. E) Il17a and Ifng expression by cells from distinct PhenoGraph clusters. F) Sample origin (left) and PhenoGraph cluster composition (right) of cells from the 30 largest TCR clonotypes. See also Figure S4.