Extended Data Fig. 10: Human thymocyte scRNAseq profiling comprising the complete double negative early progenitor to single positive trajectory. Human IELp-like cells features and relative abundance during fetal and post-birth stages in the thymus.

(a) Human thymocyte scRNA-seq profiling. Top; relative positioning of the annotated cell subsets along the complete thymocyte developmental trajectory. Bottom; heatmap highlighting mRNA scaled gene-wise (relative to maximum per gene) expression of indicated genes. (b, c) Violin plots showing leukocyte trafficking receptors and T cell markers expression pattern among human thymocytes. Data shown are imputed and normalized log transformed expression values. The human thymocyte scRNA-seq analysis shown was generated mining a validated and publicly available data set comprising first and second trimester, as well as post-birth thymus specimens published by Jong-Eun Park, et al.³¹. SMC = smooth muscle cells. The subset annotation shown in the figure was originally published by the authors. (d) % of gut homing human IELp-like among DN (early) thymocytes in sample comprising first and second trimester, as well as post-birth thymus specimens. No third trimester specimens were available in this data set. Human IELp-like cells are here defined as; CD34+, MPO+, CD7+, MME^low/−, and CD1A−; and those that are imprinted with a gut homing signature are triple positive for ITGA4, ITGB7 and SSTR2. ND = not detected.