Fig. 2

Pax9 and Msx1 have non-overlapping expression patterns in the pharyngeal arches. A–F Pax9^Cre and Msx1^Cre−ERT2 mice were mated with R26R^lacZ reporter mice and embryos were stained with X-Gal at E10.5. A–C Pax9^Cre;R26R^lacZ embryo showing Pax9 expression in the pharyngeal endoderm (PE) in the whole embryo (A) and in coronal sections (B, C). D–F Msx1^Cre−ERT2;R26R^lacZ embryo showing expression in presumed neural crest cells (NCC) in the pharyngeal mesenchyme in the whole embryo (D) and in sagittal (E) and coronal (F) sections. Pharyngeal arches are numbered. Scale bars: 500 µm in A, B, D, E, 50 µm in C, F. G–I Single cell transcriptomic data from E9.5 caudal pharyngeal arches was analysed for expression of marker genes to identify specific cell types (G). Pax9 and Msx1 expression was present in only three cells (H) and the majority of Msx1 cells expressed the NCC markers Hoxa2 and Pax3 (I). A subset of cells also expressed smooth muscle cell markers Tagln and Pdgfrb