Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

Embryonic mouse diaphragm is a primary model for studying myogenesis and neuro-muscular synaptogenesis, both of which represent processes regulated by spatially organized genetic programs of myonuclei located in distinct myodomains. However, a spatial gene expression pattern of embryonic mouse diaphragm has not been reported. Here we provide spatially resolved gene expression data for horizontally sectioned embryonic mouse diaphragms at E14.5 and E18.5. These data reveal gene signatures for specific muscle regions with distinct maturity and fiber type composition, as well as for a central neuromuscular junction and a peripheral myotendinous junction compartments. Comparing spatial expression patterns of wild type mice with those of mouse mutants lacking either the skeletal muscle calcium channel CaV1.1 or b-catenin, reveals curtailed muscle development and dysregulated expression of genes potentially involved in NMJ formation. Altogether, these datasets provide a powerful recourse for further studies of muscle development and NMJ formation in the mouse embryo. Overall design: Three E14.5 and two E18.5 diaphragm muscles from control embryos, one E14.5 and one E18.5 diaphragm from Cav1.1 KO and one E18.5 diaphragm from bCat cKO embryo were analyzed by FFPE Visium Spatial Transcriptomics