Fig. 2: Transcriptomic characterization of iPSc-derived TEPs.

a Bulk RNA-seq across iPSc-to-TEP differentiation, with samples from D0 (iPSc) to D14–D22 (TEPs). Heatmap shows log2-normalized expression of genes grouped into nine co-regulated modules defined by differential expression versus D0 iPSc (Left). Primary human TECs were included as controls. GO terms enriched in each gene module were identified using ClusterProfiler (v3.18.1) and arranged by shared gene similarity (Right). The network was plotted in Cytoscape (v3.8.x) with orientation forced along the differentiation timeline, yielding a graph of significant biological processes enriched at each stage. DE Definitive Endoderm, AFE Anterior Foregut Endoderm, 3PPE Third Pharyngeal Pouch Endoderm, TEP Thymic Epithelial Progenitor. (Created in BioRender. Guillonneau, C. (2025) https://BioRender.com/cx6622l). b Cell-type deconvolution of the D16 differentiation end product against the Magaletta et al. scRNA-seq atlas of pharyngeal organogenesis. Deconvolution method: MuSiC (MuSiC_prop(), default parameters), outputs shown as estimated proportions per reference cell type (n = 6, from independent differentiations, statistics: mean + standard deviation). Source data are provided as a Source Data file.