Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis [DevMap_mouse_E10.0-R1]

Here we use PEtracer, a prime-editing based molecular recorder that continuously installs heritable genetic marks at engineered target sites as cells divide, to reconstruct high-resolution lineage trees across mouse embryogenesis.

Profiling over 1.5 million cells from 16 embryos collected at half-day intervals from E7.5 to E10.0, we reconstruct lineage trees that resolve approximately 75% of cell divisions and pair each tree with deep single-cell transcriptional profiling. Combining lineage and transcriptional information, we chart the landscape of cell fate decisions during gastrulation and early organogenesis, quantifying cell fate biases, the timing of fate restriction, progenitor pool sizes, and lineage relationships across the embryo.