Fig. 2. Identification of a novel RORγt⁺ APC lineage.

a, Schematic of paired scRNA-seq and scATAC-seq of Lin^–RORγt⁺MHCII⁺ cells from the mLN of 2-week-old Rorc^{Venus-creERT2} mice (pooled from 16 biological replicates). b,c, Uniform manifold approximation and projection (UMAP) visualization of 10,145 cells profiled by scRNA-seq (b) or scATAC-seq (c), coloured by cluster annotation. d, Dot plot showing the expression of canonical ILC3 or cluster I–IV marker genes e, Similarity between cell types identified in b and ImmGen bulk microarray profiles for immune and stromal cells. Cell lineages in which any individual cell type exhibited a cosine similarity greater than 0.25 were included in the visualization. f, scRNA-seq UMAP overlaid with imputed expression of Aire. g, Similarity between Thetis cell subsets in b and thymic epithelial subsets from publicly available single-cell transcriptomic data (cTEC; cortical thymic epithelial cell).