Minoxidil and PGE ₂ treatments reprogram mesenchymal cell state trajectories and hematopoietic, epithelial, and endothelial transcriptional profiles in small thymuses. (A) Cell state trajectory mapping of mesenchymal differentiation in E13–13.5 embryonic thymuses were compared after carrier and drug treatments in the pregnant mice. The mesenchymal cluster trajectories were compared in control Tbx1^+/+-carrier and Tbx1^neo2/neo2-carrier, -minoxidil, or -PGE₂ groups. Black circles indicate key decision points where the differentiation trajectory branches into multiple possible fates. Grey circles represent sequential progression of cells through differentiation, without any major fate change. The numbers label the sequential order of the cell states with state 1 the earliest, and higher numbers representing later stages. (B–D and F–H) The DEGs from the scRNA data were compared among various non-mesenchymal cells, including hematopoietic subclusters, TEC subclusters, and the one endothelial subcluster isolated from E13–13.5 Tbx^1+/+ and Tbx1^neo2/neo2 embryos following the indicated carrier, minoxidil, and PGE₂ treatments administered to the pregnant mice. Heat maps revealed the relative expression of the key transcripts for the following populations: (B) hematopoietic subclusters, (C) TEC subclusters with transcripts involved in thymopoiesis, and (D) Sox family members in TECs. (E) The expression scaling used in B–D. (F–H) The single endothelial subset was compared for the following: (F) Sox family member TFs, (G) additional transcriptional regulators and, (H) angiogenic genes. The DEGs shown in B–D and F–H were selected based on a P < 0.00001, and logbase2 differences >1.0 were shown.