Digital reconstruction of spatiotemporal atlas unveils the cellular origins and signaling networks underlying early mouse organogenesis

Spatiotemporal gene expression and signaling orchestration are pivotal for shaping the patterns of early embryonic development. Here we profiled 360 serial sections (10-mm thickness) across 6 whole embryos during early organogenesis to generate a comprehensive spatial transcriptomic map at single-cell resolution. We developed SEU-3D to reconstruct "digital embryos", providing a virtual representation and investigation of regionalized gene expression in its native spatial context. By combining these measurements with space-informed gene-cell co-embedding analysis, we have systematically characterized the spatial atlas of endoderm and mesoderm over time, elucidating the intricate networks of cell signaling that traverse germ layers and cell types. Furthermore, we observed regionalized identity of cells along the anterior boundary between embryonic and extra-embryonic tissues of the cardiac crescent, which reflects their cellular origins, and the coordinated signaling further patterning these cells into cardiac-specific territories. Collectively, the reconstruction of single-cell resolution whole “digital embryo” provides significant insights into early mouse organogenesis, offering a unique platform for future investigations into the mechanisms underlying embryonic development. Stereo-seq on whole mouse embryos at E7.5, E7.75 and E8.0 stages (replicates per stage). Replicates were OCT-embeded and sequenced together. Samples were collected by sereal coronal sections of 10-µm thickness.