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Spatial transcriptomic maps of whole mouse embryos

ABSTRACT: Precise spatiotemporal orchestration of gene expression is required for proper embryonic development. The application of high throughput single-cell technologies have provided comprehensive transcriptomic definitions of cell states within the embryo, but our knowledge of their spatial localization remains elusive. To explore early mouse organogenesis, we used Slide-seq to generate high-resolution maps of whole E8.5 and E9.5 mouse embryos. We developed sc3D, a tool for creating a three-dimensional (3D) 'digital embryo,' which allowed us to quantitatively decipher regionalized gene expression across multiple tissues. Our transcriptomic atlas facilitated us to characterize gene expression patterns along the anteroposterior and dorsoventral axes, with a particular emphasis on neural tube development. We nominated and functionally characterized Prdm8, a histone methyltransferase, as a neural tube patterning gene. Furthermore, we were able to determine the transcriptional identity of ectopic neural tubes in a classical Tbx6 mutant, which provided us with additional insights into neural tube patterning. Taken together, we combined computational and experimental tools to generate a framework that enables systematic spatiotemporal dissection of complex embryonic structures via high-throughput profiling of molecular phenotypes, thereby paving the way for the investigation of congenital and developmental abnormalities.

ORGANISM(S): Mus musculus

PROVIDER: GSE197353 | GEO | 2022/02/28

REPOSITORIES: GEO

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