Fig. 3: Cellular diversity of iNKT cells at ST0.

a t-SNE plots from scRNA-seq dataset from sorted ST0 iNKT precursors (iNKTp). b Feature plots depicting specific gene expression in each cluster in ST0 iNKTp. c Feature plot depicting single-cell gene expression of Cd4, Cd8a and their co-expression (top). Bar graph represents the average (Ave) expression of Cd4 and Cd8a in the clusters (bottom). d Representative flow plots of CD4 vs CD8 expression. The bar graph represents means ± SD, n = 19. Data represent seven independent experiments (bottom). DP CD4⁺CD8⁺ double positive, DN CD4⁻CD8⁻ double negative, CD4^SP CD4⁺ single positive. e Violin plots of Cd8 expression in each cluster-derived ST0 iNKT cells from C57BL/6 mouse (red) and rec-Vα14Tg mouse (green). f The ordering of ST0 iNKTp along pseudotime in a state-space defined by Monocle 3. Each color represents a cluster. g The same pseudotime plot as in (f), feature plots depicting single-cell gene expression trajectory of Ccr7 in ST0 iNKTp development (left). The bar graph represents Ave expression of Ccr7 (right). h Representative flow plots of Ccr7 expression in ST0 iNKTp (left). Bar graph presents mean CCR7⁺ iNKT ± SD, n = 3 (right). i, l Aggregate scATAC-seq browser tracks for Zbtb16 (i) and Rorc (l) in ST0 iNKTp clusters. The bar graph represents Zbtb16 (i) and Rorc (l) Ave expression (right). j, m The same pseudotime plot as in f; feature plots depicting single-cell gene expression of Zbtb16 (j) and Rorc (m) in the ST0 iNKTp development trajectory. k, n Representative flow plots of PLZF (k) and RORγt (n) expression patterns in ST0 iNKTp (bottom). Bar graphs represent mean PLZF⁺ iNKT ± SD (k) and mean RORγt⁺ iNKT ± SD (n) (top). n = 5, data represent three independent experiments.