Digital reconstruction of full embryos during early mouse organogenesis Article Swipe
Peng Xie
,
Juan Shen
,
Yi Yang
,
Xinrui Wang
,
Wei Liu
,
Hailong Cao
,
Yanying Zheng
,
Chen Wu
,
Guangyao Mao
,
Linjin Chen
,
Jingjing He
,
Weiheng Zheng
,
Zehong Yang
,
Xiao Zhang
,
Xu Jiang
,
Xianfa Yang
,
Ke Fang
,
Yan Liu
,
Xin Xue
,
Xueting Chen
,
Chaoyi Wang
,
Xing Liu
,
Ling Liu
,
Xuebiao Yao
,
Naihe Jing
,
Wei Xie
,
Jin Liu
,
Hua Cao
,
Zhuojuan Luo
,
Xiaodong Fang
,
Chengqi Lin
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1016/j.cell.2025.05.035
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1016/j.cell.2025.05.035
Early organogenesis is a crucial stage in embryonic development, characterized by extensive cell fate specification to initiate organ formation but also by a high susceptibility to developmental defects. Here, we profiled 285 serial sections from six E7.5-E8.0 embryos to generate full spatiotemporal transcriptome and signal maps during early organogenesis at single-cell resolution. By developing SEU-3D, we reconstructed digital embryos, enabling investigation of regionalized gene expression in the native spatial context. We established a space-informed gene-cell co-embedding approach, systematically characterized the spatial atlas of endoderm and mesoderm derivatives, and elucidated signaling networks across germ layers and cell types. Furthermore, we characterized a primordium determination zone (PDZ) formed along the anterior embryonic-extraembryonic interface at E7.75, and it revealed that the coordinated signaling communications contribute to the formation of cardiac primordium. Collectively, the high-resolution "digital embryo" provides significant insights into early organogenesis and a unique spatial platform for studying development and diseases.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1016/j.cell.2025.05.035
- https://www.cell.com/action/showPdf?pii=S0092867425006221
- OA Status
- hybrid
- Cited By
- 5
- References
- 109
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4411412223
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4411412223Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1016/j.cell.2025.05.035Digital Object Identifier
- Title
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Digital reconstruction of full embryos during early mouse organogenesisWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
-
2025-06-18Full publication date if available
- Authors
-
Peng Xie, Juan Shen, Yi Yang, Xinrui Wang, Wei Liu, Hailong Cao, Yanying Zheng, Chen Wu, Guangyao Mao, Linjin Chen, Jingjing He, Weiheng Zheng, Zehong Yang, Xiao Zhang, Xu Jiang, Xianfa Yang, Ke Fang, Yan Liu, Xin Xue, Xueting Chen, Chaoyi Wang, Xing Liu, Ling Liu, Xuebiao Yao, Naihe Jing, Wei Xie, Jin Liu, Hua Cao, Zhuojuan Luo, Xiaodong Fang, Chengqi LinList of authors in order
- Landing page
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https://doi.org/10.1016/j.cell.2025.05.035Publisher landing page
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https://www.cell.com/action/showPdf?pii=S0092867425006221Direct link to full text PDF
- Open access
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YesWhether a free full text is available
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-
hybridOpen access status per OpenAlex
- OA URL
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https://www.cell.com/action/showPdf?pii=S0092867425006221Direct OA link when available
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Biology, Organogenesis, Embryo, Cell biology, Computational biology, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
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5Total citation count in OpenAlex
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2025: 5Per-year citation counts (last 5 years)
- References (count)
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109Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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