Three-dimensional molecular architecture of mouse organogenesis

Mammalian embryos exhibits sophisticated cell organizations that are intricately orchestrated at both molecular and cellular level. It has recently become apparent that cells within the animal body display significant heterogeneity, both in terms of their cellular properties and their spatial distributions. However, current spatial transcriptomics profiling either lack three-dimensional representation or are limited in their ability to capture the complexity of embryonic tissues and organs. Here, we present a represented spatial transcriptome atlas of all major organs at embryonic day 13.5 (E13.5) in the mouse embryo, and provide a three- dimensional rendering of molecular regulation for embryonic patterning with stacked sections. By integrating this spatial transcriptome data with corresponding single-cell transcriptome data, we offer a detailed molecular annotation of the dynamic nature of organ development, spatial cellular interaction, embryonic axes and divergence of cell fates underlying mammalian development, which would pave the way for precise organ engineering and stem cell-based regenerative medicine. Organogenesis stage (embryonic day 13.5, E13.5) embryos were collected of C57BL/6 mice, and embryos images were taken for recording and conformation of developmental staging. Collected embryos were embedded in Tissue freezing medium and stored at -80C until sectioning. The whole embryo tissue was serially cryo-sectioned along craniocaudal axis at 10m, and about 1000 sections were harvested. Considering the morphology and uniform sampling, 10 sections from a male embryo and 4 sections from a female embryo were selected for spatial transcriptomic analysis by 10x Genomics Visium platform.哺乳动物胚胎展现出高度精密的细胞组织结构，其在分子与细胞层面均受到精细调控。近期研究表明，动物体内的细胞无论在细胞特性还是空间分布上，均呈现出显著的异质性。然而，当前的空间转录组学（spatial transcriptomics）分析技术要么缺乏三维表征能力，要么难以完整捕获胚胎组织与器官的复杂特性。 本研究构建了小鼠胚胎发育第13.5天（E13.5）所有主要器官的代表性空间转录组图谱，并通过堆叠切片实现了胚胎模式形成的分子调控机制的三维可视化呈现。 通过将该空间转录组数据与对应单细胞转录组（single-cell transcriptome）数据进行整合，我们对哺乳动物发育过程中器官发生的动态特征、空间细胞互作、胚胎轴线以及细胞命运分化进行了详尽的分子注释，该成果将为精准器官工程及基于干细胞的再生医学奠定重要基础。 本研究收集了C57BL/6小鼠的器官发生期（胚胎发育第13.5天，E13.5）胚胎，并拍摄胚胎图像以记录并确认发育阶段。收集的胚胎经组织冷冻包埋剂包埋后，于-80℃储存直至切片。将完整胚胎组织沿头尾轴以10 μm厚度进行连续冰冻切片，共收获约1000张切片。考虑到样本形态与采样均匀性，我们从1个雄性胚胎中选取10张切片、从1个雌性胚胎中选取4张切片，通过10x Genomics Visium平台开展空间转录组学分析。