Year: 2023
Type: article
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.
Source: Nature Genetics
Institutions: Max Planck Institute for Molecular Genetics, Technische Universität Berlin, Broad Institute, Freie Universität Berlin, Harvard University, Massachusetts General Hospital, Centre National de la Recherche Scientifique, Université de Toulon, Aix-Marseille Université, Laboratoire d’Informatique et Systèmes
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $11,690
Funders: U.S. Department of Health and Human Services, Burroughs Wellcome Fund, Aix-Marseille Université, Agence Nationale de la Recherche, Max-Planck-Gesellschaft, National Institutes of Health, Harvard Stem Cell Institute, National Institute of Mental Health, National Human Genome Research Institute
OpenAlex ID: W4383340946