Extended Data Fig. 4: Cross-dataset integration confirms conserved ThyMC subsets in human and mouse.

(A) UMAP representation of conos joint embedding showing overlap between our human samples (colored dots) and a publicly available human dataset (gray dots). ThyMCs colored by origin (left). Overlays of individual population markers (right) indicate transcriptionally similar populations between the two sample sets. (B) UMAP of a joint conos embedding with our mouse dataset (blue dots) and publicly available mouse samples (orange dots) demonstrating significant overlap in identified populations (left panel). Annotation of CD248+ ThyMCs, Penk+ ThyMCs and Postn+ ThyMCs on joint UMAP representation of our mouse cells and a publicly available dataset (right panel). (C) UMAPs showing the expression of marker genes Cd248, Penk, and Postn that define each ThyMC subtype presented as joint conos embeddings with our dataset and publicly available mouse samples. (D) Conos joint embedding UMAP showing clustering of ThyMCs from a publicly available mouse dataset (orange dots) and our mouse samples (blue dots) (left panel). Annotation of CD248+ ThyMCs, Penk+ ThyMCs and Postn+ ThyMCs on joint UMAP representation of our mouse cells and a publicly available dataset (middle panel). Joint UMAP showing the annotation of ThyMCs identified by Handel et. al (right panel). (E) UMAPs showing the expression of marker genes Cd248, Penk, and Postn that define each ThyMC subtype presented as joint conos embeddings with our dataset and the mouse dataset published by Handel et al.