Single-cell RNA-seq atlas of mouse embryos during gastrulation

Specifically, we generated embryos using CAST/EiJ × C57BL/6J F1 sperm, such that the resulting progeny inherit a random assortment of highly polymorphic CAST alleles, while females retain a CAST-derived X chromosome that enables allelic assignment.

In total, we collected 95 embryos spanning embryonic day (E)6.5 to E9.0, capturing developmental progression from the onset of primitive streak formation through the establishment of early organ fields. We clustered cells using an approach that accommodates the presence of shared transcriptional states across multiple developmental time points while retaining rare but transcriptionally distinct populations, such as primordial germ cells (PGCs).