Collagens, ECM, and angiogenic transcripts are altered in the six mesenchymal cell subsets from hypoplastic lobes. (A and B) Fetal thymuses were isolated from Tbx1^+/+ and Tbx1^neo2/neo2 E13–13.5 embryos from carrier, minoxidil-, and PGE₂-treated pregnant mice. ScRNA Seq revealed substantial transcriptome differences with the six mesenchymal cell clusters. (A) A heat map was used to visualize collagen and ECM transcript differences among the six mesenchymal clusters between control (Tbx1^+/+-carrier) versus hypoplastic lobes from the (Tbx1^neo2/neo2-carrier) and the corresponding genotypes following in vivo minoxidil or PGE₂ administration. These were separated into three distinct clusters. (B) A separate heat map was established comparing the transcript levels for genes coupled to angiogenic pathways. These were separated into four clusters. The relative z-score and identification of the mesenchymal subclusters are illustrated. (C) Heat maps reveal the relative expression of the indicated mesenchymal transcripts grouped under angiogenic regulators. In A–C, genes with P < 0.00001 and logbase₂ differences >1.5 are shown. (D) The thymic cellularity and splenic T/B cell ratios were determined from E18–18.5 embryos obtained from the indicated carrier and minoxidil treatment groups. Tbx1^+/+-carrier (n = 15), Tbx1^+/+-minoxidil (n = 4), Tbx1^neo2/neo2-carrier (n = 6), and Tbx1^neo2/neo2-minoxidil (n = 3). Statistical analyses was performed with one-way ANOVA (Brown–Forsythe and Welch tests).