Extended Data Fig. 2: Characterization of T cell subsets by scRNA-seq and FACS in LNs and the diseased arterial wall.

a, Heatmap shows the top 10 DEGs in each T cell subtype. b, Marker combinations define 10 T cell subtypes in Violin plots. Foxp3 for T_reg T cells, Cd44 for effector/memory T cells, Sell (L-selectin or CD62L) and Ccr7 for naïve T cells, Klrb1c (Killer cell lectin-like receptor) for natural killer T- (NKT) cells, Tcrg-C1 (TCRγ constant region) for γδ T cells, and Gzmk (Granzyme K) for CD8 effector T cells. Subset 1: CD4 effector regulatory (eT_reg) T cells (Cd4⁺Foxp3⁺Cd44⁺Sell⁻Ccr7^low); subset 2: CD4 T_em T cells (Cd4⁺Foxp3⁻Cd44⁺Sell⁻Ccr7^low); subset 3: CD8+ T_em T cells (Cd8a⁺Cd44⁺Sell⁻Ccr7^low); subset 4: CD8 naïve T cells (Cd8a⁺Cd44⁻Sell⁺Ccr7^high); subset 5: CD8+ T_cm T cells (Cd8a⁺Cd44⁺Sell⁺Ccr7^int); subset 6: NKT/CD8 T_cm T cells (Cd8a⁺Cd44⁺Sell⁺Ccr7^intKlrb1c⁺); subset 7: CD4 naïve T cells (Cd4⁺Cd44⁻Sell⁺Ccr7^highLy6c1⁻); subset 8: CD4 central T_reg (cT_reg) T cells (Cd4⁺Foxp3⁺Ccr7^low); subset 9: γδ T cells (Cd4⁻Cd8a⁻Tcrg-C1⁺Trdc⁺); subset 10: CD4 T_cm T cells (Cd4⁺Cd44⁺Sell⁺Ccr7^highLy6c1⁺); each dot represents one cell. c, The percentages of T cell subtypes in LNs, ATLOs and plaques of aged WT and Apoe^-/- mice were determined by FACS. Protein marker combinations were used to define T cell subtypes: CD4 naïve T cells (CD4⁺CD44⁻CD62L⁺), CD8 naïve T cells (CD8⁺CD44⁻CD62L⁺); CD4 T_reg (CD4⁺Foxp3⁺) T cells, CD8 T_cm (CD8⁺CD44⁺CD62L⁺) T cells, CD8 T_em (CD8⁺CD44⁺CD62L⁻) T cells, CD4 T_cm (CD4⁺Foxp3⁻CD44⁺CD62L⁺) T cells and CD4 T_em (CD4⁺Foxp3⁻CD44⁺CD62L⁻) T cells. WT LNs (n = 4), Apoe^-/- LNs (n = 12), ATLOs (n = 6), plaques (n = 6), Data are mean ± s.e.m. One-way ANOVA with Bonferroni post hoc test was used to perform statistical analysis.

Source data