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. 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小鼠胚胎膈肌是研究肌发生与神经肌肉突触形成的经典模型，这两类过程均由定位于不同肌域的肌细胞核的空间有序遗传程序所调控。然而，目前尚无关于小鼠胚胎膈肌空间基因表达图谱的研究报道。本研究提供了E14.5及E18.5时期水平切片的小鼠胚胎膈肌的空间分辨基因表达数据。该数据揭示了具有不同成熟度与肌纤维类型组成的特定肌肉区域的基因特征，同时也揭示了中央神经肌肉接头（neuromuscular junction，NMJ）区域与外周肌腱接头区室的基因特征。通过对比野生型小鼠的空间表达模式与分别缺失骨骼肌钙通道CaV1.1或b-连环蛋白（b-catenin）的小鼠突变体的空间表达模式，可发现肌肉发育受损以及潜在参与NMJ形成的基因表达失调。综上，本数据集可为小鼠胚胎肌肉发育及NMJ形成的后续研究提供有力的研究资源。本研究采用福尔马林固定石蜡包埋（FFPE）样本的Visium空间转录组（Visium Spatial Transcriptomics）技术，对如下样本进行了分析：3份来自对照胚胎的E14.5时期膈肌样本、2份E18.5时期对照胚胎膈肌样本，1份E14.5时期及1份E18.5时期Cav1.1基因敲除（KO）胚胎膈肌样本，以及1份E18.5时期bCat条件性敲除（cKO）胚胎膈肌样本。