GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE342nnn/GSE342272/primary200OKTranscriptomicsMus musculus OtherExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE342272GEOGSEfalseComprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis [DevMap_mouse_E9.5-R3]Mammalian development proceeds through a series of cell fate decisions that transform a single zygote into a complex embryo, yet the lineage relationships underlying these decisions have been difficult to resolve in vivo. 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. These analyses reveal strikingly reproducible lineage architecture across replicate embryos despite the regulative flexibility of mammalian development, establishing a quantitative framework for how cell fate is allocated in vivo. This submission is one of 16 per-embryo Series grouped into a single SuperSeries for the DevMap project.2026/09/01GSE342272GSM9927017GSM992701834290342272Mus musculus