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Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis.
Sampath Kumar, Abhishek; Tian, Luyi; Bolondi, Adriano; Hernández, Amèlia Aragonés; Stickels, Robert; Kretzmer, Helene; Murray, Evan; Wittler, Lars; Walther, Maria; Barakat, Gabriel; Haut, Leah; Elkabetz, Yechiel; Macosko, Evan Z; Guignard, Léo; Chen, Fei; Meissner, Alexander.
Afiliación
  • Sampath Kumar A; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • Tian L; Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
  • Bolondi A; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Hernández AA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • Stickels R; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • Kretzmer H; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
  • Murray E; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Wittler L; Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA.
  • Walther M; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • Barakat G; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Haut L; Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • Elkabetz Y; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • Macosko EZ; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • Guignard L; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  • Chen F; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
  • Meissner A; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
Nat Genet ; 55(7): 1176-1185, 2023 07.
Article en En | MEDLINE | ID: mdl-37414952
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Organogénesis / Transcriptoma Límite: Animals Idioma: En Revista: Nat Genet Asunto de la revista: GENETICA MEDICA Año: 2023 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Organogénesis / Transcriptoma Límite: Animals Idioma: En Revista: Nat Genet Asunto de la revista: GENETICA MEDICA Año: 2023 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Estados Unidos