Fig. 2: Single-cell RNA sequencing of freshly isolated TEC defines common cell clusters to mTEC and cTEC that are maintained in vitro.
a UMAP visualisation of the cellular composition of the human post-natal thymus by clusters indicated by colours and numbers from 1 to 15 describing the heterogeneity of cTEC (1–3) and mTEC (7-11). Clusters 12–15 were common to cortex and medulla (comTEC); clusters 4–6 described residual immune cells (PMNs, DCs and thymocytes). b UMAP representation of the same thymic cells indicating main subgroups (cTEC, cortical epithelial cells, in green; mTEC, medullary epithelial cells, in red; TEC cells with common features, in brown and residuals of immune cells in grey). c Area under the curve (AUC) summary intensity plots for the gene signatures of cTEC (CCL25, CD274, CFC1, CTSV, FOXN1, KCNIP3, LY75, PRSS16, PSMB11, SCX, SLC46A2, TBATA and TP53AIP1), mTEC (CD24, CDH1, CLDN3, EPCAM and HES6) and comTEC (CCL19, CFTR, COL1A1, DAB2, FN1, GLIPR2, HAS2, HGF, KRT14, KRT15, LOXL2, MKI67, MMP2, S100A4, SNAI1, SNAI2, TFCP2L1, TGFB3, TGFBR2, THY1, TP63, TWIST1 and ZEB1) clusters showing expression level for lineage specific genes in a purple scale. Single-cell expression values are represented as calculated median intensity of area under the curve. d Heatmap and hierarchical clustering of cultured cTECType1 (green, n = 3), mTECType1 (red, n = 3) and cultured unsorted TEC (black, n = 2) according to main genes clusters defined in single-cell RNA sequencing. Genes list is displayed on the right and includes comTEC signatures (epithelial-to-mesenchymal transition (EMT), polykeratins and proliferative - clusters 12-13-14) and specialised cell clusters: Myo (clusters 7-8), Neuro (clusters 9–10), Ionocytes (cluster 15) and differentiated mTEC (cluster 11).
