Fig. 5: Early phase of hTO differentiation.

a Reaggregation of iPSc-derived TEPs with primary human ETPs to form hTOs (human Thymic Organoids) cultured in a 3D fibrin hydrogel at an air-liquid interface in medium supplemented with RANKL, IL7, SCF, and FLT3L (Created in BioRender. Guillonneau, C. (2025) https://BioRender.com/apk8n61). b Bright-field images of hTOs (human Thymic Organoids) at 24 h and D4 showing a compact spheroid core with a peripheral cellular crown (identical magnification) (n = 12 from independent differentiations and ETP donors). c scRNA-seq of EPCAM⁺CD45⁻ cells from D7 organoids with UMAP embedding and cell-cycle scoring (10x Genomics; Seurat workflow). d Module score for a TEP gene set: PDPN, PAX9, IL7, EBF1, FN1. e Integration of the EPCAM⁺CD45⁻ scRNA-seq dataset (Clusters 1, 2, and 3) with the Bautista human TEC atlas; with reference cells in gray. f Cell type deconvolution of TEPs and CD205⁺ TEPs against the EPCAM⁺CD45⁻ scRNA-seq dataset. g Distribution of the Tau tissue-specific variability index within clusters 3 and 1. Tau was computed from GTEx tissue expression data; TRA enrichment was assessed on the top-200 cluster-specific genes. Source data are provided as a Source Data file. h Assessment of the TRA repertoire in Cluster 3, showing enrichment for brain antigens. Source data are provided as a Source Data file.