Fig. 1

iNKT cells are skewed to NKT1 phenotype in SKG ZAP70 mutant mice. a Gene set enrichment analysis of 216 TCR signaling pathway-related genes comparing the transcriptomes of thymic NKT1 and NKT2 cells from BALB/c mice. b Differentially expressed TCR pathway genes enriched in NKT1 cells from triplicate RNA-seq runs are shown in a heatmap. c–e Decreased thymic iNKT cells in SKG mice. c Representative staining of iNKT cells gated as TCRβ^int, CD1d-αGC tetramer⁺ cells in live, CD8-negative thymocytes from WT and SKG mice. d Percentages and e absolute numbers of thymic iNKT cells in the WT and SKG mice. f iNKT cell subsets were gated as PLZF^lo RORγt⁻ (NKT1), PLZF^hi RORγt⁻ (NKT2), and PLZF^intRORγt⁺ (NKT17). g Percentages in total iNKT cells and h absolute numbers of the iNKT cell subsets in WT and SKG mice. i, j Expression of the indicated transcription factors and surface markers CXCR3 (NKT1 marker) and PD-1 (NKT2) marker in total WT or SKG iNKT cells. k Innate-like CD8 T cells, gated as Eomes⁺ CD122⁺ in CD8⁺CD3ε^hi thymocytes. l Absolute numbers of innate-like CD8 T cells in WT and SKG mice. m Thymic iNKT cell subsets from mixed bone marrow chimera mice. Percentages of iNKT subsets from either WT (CD45.1) or SKG (CD45.2) donors were plotted. c–m Data are representative from one of at least three independent experiments. Graphs represent mean ± SD with symbols representing individual mice. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001; n.s. not significant (unpaired two-tailed Student’s t test)