Figure 3.
The temporal dynamics of mTEC diversity during thymus organogenesis. (A) UMAP visualization of 5,493 mTECs with 9 subclusters. (B) Percentages of 8 mTEC subtypes across the development from E13.5 to adult. (C) UMAP visualization of the expression of curated feature genes specific for 4 mTEC subtypes. (See also Figure S3A .) (D) Single-molecule RNA fluorescence in situ hybridization in fetal thymus slides with probes targeting Foxn1 and Ccl21a. (E–H) Immunofluorescence staining of 5-week thymus slides with antibodies to Krt5, Emp2 (E), Hnf1a (F), Ascl1 (G), Cdx1 (H), and Krt8 (C, cortex; M, medulla). (I) UMAP visualization of the expression of curated feature genes specific for 4 mTEC subtypes: Spink5+ cells, Bpifa1+ cells, tuft-like cells, and Ccl6+ cells. (See also Figure S4A ) (J) Immunofluorescence staining of 5-week thymus slides with antibodies to Krt5 (green), Ccl6 (red), and Krt8 (blue). All staining experiments were replicated at least 2 times, with 2 biological replicates for each experiment.