A Single-Cell Transcriptomic Atlas of Symmetry Breaking in Sheep
The mammalian body plan is established during symmetry breaking and gastrulation. In ungulates and primates, these events occur within a flat embryonic disc and coincide with the developmental window most susceptible to pregnancy loss. Using the EvercodeTM Cell Fixation kit v2 (ECF2101, Parse Biosciences), we have  generated a single-cell RNA sequencing atlas of in vivo sheep embryos that defines the timing and molecular programs underlying lineage segregation, as well as the inter-lineage signalling mediating anterior visceral hypoblast specification (AVH) and primitive streak formation. Overall design: We collected single cells cells from eight pooled samples, comprising 80 in vivo-derived embryos collected from superovulated ewes between embryonic day (E) 11, prior to symmetry breaking and onset of gastrulation, and 13.5, after gastrulation but before neural folding and somitogenesis. The dataset included E11 and E11.5 whole embryos (spherical and ovoid), as well as isolated embryonic discs (EDs) with surrounding extraembryonic membranes (EEMs) from E12.5 and E13.5 (tubular and filamentous) conceptuses. Sequencing was performed on Illumina NovaSeq 6000. Two sublibraries were generated.