Parallel scRNA-seq and genetic recording reveals lineage decisions in early mouse embryogenesis

How cell fate is specified at early stages of development is a fundamental question in biology. We apply deep transcriptomic profiling to map cell lineages at single cell resolution in embryoid bodies (EBs); a spontaneous, manipulatable, in vitro system for embryonic development. We predict the overall cell fate trajectory and define the transcriptomic landscape of cells at each critical branch. We present a dual barcoding system, comprising a static cellular barcode and inducible genetic recorder, and leverage long-read sequencing to obtain both barcodes and transcriptome from each single cell. Using this system, we confirm overall trajectory architecture, and validate key branch points, including the early isolation of the primordial germ cell (PGC) like lineage from preimplantation epiblast-like cells. Our data suggest DNA methylation is a critical determinant of PGC cell fate choice before the postimplantation epiblast cell state is determined. Together, our data provide a high resolution lineage decision map in an organoid model of early embryogenesis, with implications for the developing embryo. Examination of single cell RNA-seq in mouse Embryoid body (EB) differentiation. Examination of single cell RNA-seq and targeted genomic DNA-seq in dual-barcode integrated EBs at day 14. Examination of single cell RNA-seq in EBs treated by 5-azacytidine or DMSO control.