Until recently, lineage tracing in mammals relied on techniques with limited precision, scope, and ability for new discovery, I will present an evolving CRISPR-Cas9 lineage tracing technology that is combined with single cell RNA-seq to produce systematic, unbiased cell fate maps with simultaneous read out of molecular phenotype. In a first application in mouse embryogenesis, the cell fate maps recapitulated canonical developmental relationships between different tissue toes and revealed the nearly complete transcriptional convergence of endodermal cells from extra-embryonic and embryonic origins. While much is learned from in vivo systems, the scale of experiments that can be achieved is limiting. We have now applied our lineage tracing technology to an in vitro model of development, embryonic trunk-like structures that self-organize from mESC aggregates to form complex structures,