Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China.
GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, 510005, Guangzhou, Guangdong, China.
The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, 510005, Guangzhou, Guangdong, China.
Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, 510530, Guangzhou, China.
Life Science and Medicine, University of Science and Technology of China, 230026, Hefei, Anhui, China.
School of Basic Medical Sciences, Guangzhou Medical University, 510005, Guangzhou, Guangdong, China.
Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China. cui_guizhong@gzlab.ac.cn.
The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, 510005, Guangzhou, Guangdong, China. suo_shengbao@gzlab.ac.cn.
Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China. peng_guangdun@gibh.ac.cn.
Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, 510530, Guangzhou, China. peng_guangdun@gibh.ac.cn.
Mammalian embryos exhibit sophisticated cellular patterning that is 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 spatial distributions. However, current spatial transcriptomic profiling either lacks three-dimensional representation or is limited in its ability to capture the complexity of embryonic tissues and organs. Here, we present a spatial transcriptomic atlas of all major organs at embryonic day 13.5 in the mouse embryo, and provide a three-dimensional rendering of molecular regulation for embryonic patterning with stacked sections. By integrating the spatial atlas with corresponding single-cell transcriptomic data, we offer a detailed molecular annotation of the dynamic nature of organ development, spatial cellular interactions, embryonic axes, and divergence of cell fates that underlie mammalian development, which would pave the way for precise organ engineering and stem cell-based regenerative medicine.
