scRNA Seq reveals transcript levels in mesenchymal, endothelial cells, epithelial, and hematopoietic subsets in embryonic thymuses after in utero carrier and drug treatments. (A) Fetal thymuses were isolated from Tbx1^+/+ and Tbx1^neo2/neo2 E13–13.5 embryos obtained from carrier, minoxidil-, and PGE₂-treated pregnant mice. scRNA Seq results were plotted with UMAPs, revealing 18 distinct cell subgroups (Tbx1^+/+-carrier, Tbx1^neo2/neo2-carrier, -minoxidil, and -PGE₂). Six mesenchymal cell clusters (M-1 to M-6), one endothelial population (En-1), five epithelial clusters (E-1 to E-5), four hematopoietic cell types (H-1 to H-4), and a red blood cell cluster (U-1) are shown. The red and orange arrows indicate the overrepresentation of M-5 and M-6 clusters in hypoplastic thymuses (Tbx1^neo2/neo2). The purple reveals changes in the M-4 cluster. (B) Dot plot comparisons reveal transcript levels in the various subclusters. Increasing dot sizes reveals the percentage of cell expression the transcripts. The orange to red scale reveals increasing expression levels. Mesenchymal (M-1 to M-6), endothelial (En-1), epithelial (E-1 to E-5), and hematopoietic (H-1 to H-4) superclusters are boxed. (C–E) Heat maps reveal the relative expression of the indicated mesenchymal transcripts grouped under three broad categories: (C) collagens/ECM proteins, (D) Sox family TFs, and (E) additional transcriptional regulators. Genes with P < 0.00001 and logbase₂ differences >1.5 are shown.