Hypoplastic thymuses from an embryonic 22q11.2 mouse model have an overrepresentation of chondrocyte markers. (A) The cardiothoracic regions are shown for E13–13.5 Tbx1^+/+, Tbx1^neo2/neo2, and Del(3/.0 Mb)/+ embryos. Black arrows point to the thymic lobes. An interrupted aortic arch in the Tbx1^neo2/neo2 and Del(3/.0 Mb)/+ embryos is shown with an open blue triangle. (B) scRNA Seq data were used to compare Sox family TFs and target collagens in six mesenchymal subsets characterized in E13–13.5 Tbx1^+/+ and Tbx1^neo2/neo2 embryos. (C) Single-cell suspensions from E13–13.5 fetal thymic lobes were analyzed by flow cytometry to monitor mesenchymal (Pdgfra) and TEC (EpCam) percentages. The cells were also analyzed for the cell surface expression of Pdgfra and Pdgfrb. (D) E13–13.5 thymic mesenchymal cells sorted from the indicated embryos were processed for RT-qPCR to determine the expression levels of the indicated collagens, ECM transcript, and the Sox5,6,9 trio. Statistical significance was determined using three independent flow sorting experiments and performing a Student’s T test. (E) A model of the developmental changes in mesenchymal subsets is presented based on the upregulation of multiple Sox family members and target genes, collagens, and the ECM gene Acan. Mes, mesenchymal cells.