Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Kumar A.†, Tian L.†, Bolondi A.†, Hernandez A., Stickels R., Kretzmer H., Murray E., Wittler L., Walther M., Barakat G., Haut L., Elkabetz Y., Macosko E.*, Guignard L.*, Chen F.*, Meissner A.*
Nature Genetics
6 juil. 2023
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 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.
