Pseudotime trajectory and TCR clonal type analyses reveal CD4 T cell differentiation and clonal expansion profiles in WT and Bhlhe40^-/- mice.

(A) Pseudotime trajectory analysis of CD4 T cell clusters in Fig 5 as conducted using Monocle 3. (B) WT and Bhlhe40^-/- CD4 T cells were binned into quartiles based on clonotype abundance. Shaded area represents the top 25% (expanders). (C) UMAP showing the expanders in WT and Bhlhe40^-/- CD4 T cell clusters. (D) Frequencies of expanders in each cluster in WT and Bhlhe40^-/- CD4 T cells.