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Journal Article

Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis

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Sampath Kumar,  Abhishek       
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Bolondi,  Adriano       
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Aragonés Hernández,  Amèlia       
Human Brain & Neural Stem Cell Studies (Yechiel Elkabetz), Dept. of Genome Regulation, (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Kretzmer,  Helene       
Computational Genomics (Helene Kretzmer), Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Wittler,  Lars       
Dept. of Developmental Genetics (Head: Bernhard G. Herrmann), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Walther,  Maria       
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Barakat,  Gabriel       
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Haut,  Leah
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Elkabetz,  Yechiel       
Human Brain & Neural Stem Cell Studies (Yechiel Elkabetz), Dept. of Genome Regulation, (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Meissner,  Alexander       
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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NatGenet_Sampath Kumar et al_2023.pdf
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Citation

Sampath Kumar, A., Tian, L., Bolondi, A., Aragonés Hernández, A., Stickels, R., Kretzmer, H., et al. (2023). Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis. Nature Genetics, 55(7), 1176-1185. doi:10.1038/s41588-023-01435-6.


Cite as: https://hdl.handle.net/21.11116/0000-000D-76F7-8
Abstract
Spatiotemporal orchestration of gene expression is required for proper embryonic development. The use of single-cell technologies has begun to provide improved resolution of early regulatory dynamics, including detailed molecular definitions of most cell states during mouse embryogenesis. Here we used Slide-seq to build spatial transcriptomic maps of complete embryonic day (E) 8.5 and E9.0, and partial E9.5 embryos. To support their utility, we developed sc3D, a tool for reconstructing and exploring three-dimensional 'virtual embryos', which enables the quantitative investigation of regionalized gene expression patterns. Our measurements along the main embryonic axes of the developing neural tube revealed several previously unannotated genes with distinct spatial patterns. We also characterized the conflicting transcriptional identity of 'ectopic' neural tubes that emerge in Tbx6 mutant embryos. Taken together, we present an experimental and computational framework for the spatiotemporal investigation of whole embryonic structures and mutant phenotypes.