Defining murine organogenesis at single cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation

During gastrulation, cell types from all three germ layers are specified and the basic body plan is established1. However, molecular analysis of this key developmental stage has been hampered by limited cell numbers and a paucity of markers. Single cell RNA sequencing circumvents these problems, but has so far been limited to specific organ systems2. Here we report single-cell transcriptomic characterisation of over 20000 cells immediately following gastrulation at E8.25 of mouse development. We identify 20 major cell types, which frequently contain sub-structure, including three distinct signatures in early foregut cells. Pseudospace ordering of somitic progenitor cells identifies dynamic waves of transcription and candidate regulators, which are validated by molecular characterisation of spatially resolved regions of the embryo. Within the endothelial population, cells that transition from haemogenic endothelial to erythro-myeloid progenitors specifically express Alox5 and its co-factor Alox5ap, which control leukotriene production. Functional assays using mouse embryonic stem cells demonstrate that leukotrienes promote haematopoietic progenitor cell generation. This comprehensive single cell map therefore can be exploited to reveal previously unrecognised pathways contributing to tissue development.