Single-cell mRNA sequencing of embryonic and extra-embryonic mesoderm and extra-embryonic structures in mouse embryo during gastrulation.

We performed scRNAseq on embryonic and extra-embryonic mesoderm cells from mouse embryo at Mid/Late Streak stage (Embryonic day 7.25) as well as on Late Bud stage (Embryonic day 7.75) microdissected amnion, chorion and allantois. We used transgenic embryos (Brachyury-Cre; mTmG) in which all mesoderm cells are converted to membrane-GFP upon Cre-mediated recombination and the rest express membrane Tomato. For all the samples, we identified clusters related to the localization in the tissue or the structures. Those results provide an atlas of early stages of morphogenesis of the maternal-fetal interface. Overall design: Cells enriched from embryonic mesoderm, extra-embryonic mesoderm, amnion, chorion and allantois from mouse Tcre-mTmG embryos. One replicate for each, except amnion, which has two replicates.