Colgan, W. N.; Koblan, L. W.; Villagrana, J.; Hou, T.-C. J.; Wang, M.; Gowri, G.; Chandler, W.; Sepulveda, L. A.; Ciftci, D.; Smolyar, K.; Young, A.; Wittler, L.; Markoulaki, S.; Loh, K. M.; Zhuang, X.; Yosef, N.; Smith, Z. D.; Weissman, J. S.

A comprehensive cell fate map of mammalian embryogenesis has remained out of reach due to the scale, cellular diversity, and non-deterministic nature of development in utero. Here, we use PEtracer to continuously install heritable genetic marks as cells divide, reconstructing lineage trees that resolve ~75% of cell divisions across >1.5 million cells from 16 mouse embryos collected at half-day intervals from E7.5-E10.0. We pair these trees with deep transcriptional profiling to chart the landscape of cell fate decisions during gastrulation and early organogenesis. Using these data, we quantify cell fate biases, restriction timing, progenitor pool sizes, and lineage relationships across the embryo, revealing strikingly reproducible lineage architecture across replicate embryos despite the regulative flexibility of mammalian development. We further show how lineage, spatial position, and signaling jointly determine fate outcomes and timing, with their relative influence varying by tissue. This dataset provides a quantitative framework for understanding cell fate specification and a lineage-resolved reference for generating and contextualizing developmental hypotheses at organismal scale.