Single-cell RNA sequencing detects stem-like CD4 T cells in Bhlhe40^-/- FRT.

WT and Bhlhe40^-/- mice were infected intravaginally with 1×10⁵ C. muridarum. Activated CD4 T cells (live CD90.2⁺CD4⁺CD44^hi) in the FRT were sorted for scRNAseq using 10x genomics 5’ GEX. (A) UMAP depicting 14 clusters of CD4 T cells from merged WT and Bhlhe40^-/- CD4 T cells (left); deconvolution of the composite UMAP into WT and Bhlhe40^-/- components. (B) Percentages of WT and Bhlhe40^-/- CD4 T cells in each cluster following normalization of the two populations into the same cell numbers. (C) Heatmap showing top 30 most upregulated genes in each cluster, and representative genes specifically expressed within each of the top 3 clusters in WT and Bhlhe40^-/- CD4 T cells are shown on the sides with violin plots depicting expression levels in each cluster. (D) Dot plots depicting Th lineage-specific cytokines and transcription factors.