Fig. 3

Clonal trafficking of CD4 + and CD8 + T cells between synovial tissue and peripheral blood. a All common clones (defined by the exact same CDR3b sequence) in CD4 + cells between ST and PB presented in the UMAP representation from panel 2b. b Cells with clones CASSPGETQYF (left panel) and CASSLSGGAGELFF (right panel) as projected in UMAP representation from 2b. c Left: DE genes between ST and PB cells sharing the same CDR3b sequence CASSPGETQYF in Pt1-JIA (Padj < 0.05, |Log2FC| > 0.5 calculated with Bonferroni corrected Wilcoxon test). Right: DE genes between ST and PB cells sharing the same CDR3b sequence. CASSLSGGAGELFF in Pt1-JIA (Padj < 0.05, |Log2FC| > 0.5 calculated with Bonferroni corrected two-sided t-test). d Number of cells with CDR3b clones CASSPGETQYF and CASSLSGGAGELFF in different clusters as identified in UMAP representation from 2b. e DE genes of all CD4 + T cells that are enriched in ST as compared to PB (Padj < 0.05,  |Log2FC| > 0.5 calculated with Bonferroni corrected two-sided t-test). f Top upregulated GO-BP pathways in CD4 + T cells that are enriched in ST as compared to PB (Padj < 0.05, Benjamini–Hochberg corrected Fisher’s one-sided exact test on differentially expressed genes). g UMAP representation of all CD4 + T cells predicted to have a motif in GLIPH2 analysis as seen in expanded versus non expanded cells. h DE genes of CD4 + T cells that are predicted to have a pattern in GLIPH2 and are enriched to ST as compared to PB. i All common clones (defined by the exact same CDR3b sequence) in CD8 + T cells between ST and PB presented in the UMAP representation from panel 2f. j Cells with clones CASRGGTSITDTQYF as projected in UMAP representation from 2f. k DE genes between ST and PB cells sharing the same CDR3b sequence CASRGGTSITDTQYF in Pt2-SP (Padj < 0.05, calculated with Bonferroni corrected two-sided t-test)