Paper Review

A new study published in Cell, titled “Digital reconstruction of full embryos during early mouse organogenesis” reconstructs the world’s first single-cell resolution "3D digital embryo" of mice using Stereo-seq - a cutting-edge high-resolution spatial whole-transcriptome profiling technology and SEU-3D platform, and for the first time revealed key signaling pathways governing the development of organ primordia such as the heart and foregut.

The embryonic development of mammals, particularly during the critical phase of early organ formation, is a complex and meticulously orchestrated process. Understanding the mechanisms underlying early embryogenesis is crucial for investigating the origins of embryonic disorders and developmental abnormalities, proving essential for preventing birth defects and related conditions.

In this research, Stereo-seq was applied to 285 serial sections from six mouse embryos (E7.5–E8.0), resulting in the identification of 104,343 high-quality cells with precise spatial coordinates. By developing SEU-3D, a visualization platform, the authors successfully reconstructed 3D "digital embryos" capable of accurately reflecting gene expression patterns and cellular states within the native embryonic milieu. Notably, the identification of a primordium determination zone (PDZ) at the anterior embryonic-extraembryonic interface at E7.75 reveals the coordinated signaling communications during cardiac primordia formation. Additionally, they mapped the spatial cell atlas of endoderm and mesoderm derivatives, uncovering complex cross-germ-layer signaling networks.

This groundbreaking study not only provides an important reference atlas for early organ development in mammals, but also establishes fundamental scientific evidence for preventing birth defects like congenital heart disease. Stereo-seq data are available in GEO under accession GSE278603. The SEU-3D algorithm and code are accessible at https://github.com/RainyBlue-w/SEU-3D

Find out more about the research: https://www.cell.com/cell/fulltext/S0092-8674(25)00622-1

About STOmics Stereo-seq:

STOmics offers the most advanced spatiotemporal multi-omics technology, enabling unbiased discovery to answer biological questions in scientific research and clinical applications. Currently, we offer spatial transcriptomics solutions, including Stereo-seq v1.3 for fresh frozen samples, Stereo-seq OMNI for FFPE samples, Stereo-seq Large Chip Designs (LCD) for centimeter-level fresh frozen samples (now up to 2cm x 3cm), and a spatial multi-omics solution - Stereo-CITE for high-plex spatial proteo-transcriptome co-detection.

https://en.stomics.tech/ 

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