Fig. 5

Clonal expansion analysis and development trajectory inferring based on combined analysis with Monocle2. A Clonal expansion status indicated by the percentage of clonal cells in each cell clusters. B TCR overlapping in CD4 + T cells and CD8 + T cells respectively. Color responded to the percentage of overlapping. C Percentage of clonal cells in each T cell subclusters across different groups. Error bars represent mean ± SEM. Colored dots represent different samples. Differences with p < 0.05 were indicated; two-sided unpaired Wilcoxon rank sum test was used for comparison. D Development trajectory of CD4 + and CD8 + T cells inferred by Monocle2, colored according to cell types (Top), and colored according to pseudotime value (Bottom). Gradient-colored arrow indicated the direction of development inferred. E Heatmap showing differentially expressed genes arranged in pseudo temporal patterns. Related GO terms revealed biological functions and representative genes in each cluster were indicated due to space limitation. F The most differentially enriched TFs between naïve CD4 + T cells and Tregs investigated by SCIENIC algorithm. Abbreviation: GO: Gene Ontology; SCIENIC: Single-cell regulatory network inference and clustering; SEM: Standard error of mean; TFs: Translational factors