Single-cell reference cell state map of early mouse development

Ontogeny describes the orchestrated assembly of a complex multicellular organism from a single totipotent zygote. As the embryo grows, proliferating cells become restricted in their fate to realize one of many encoded phenotypes, which are subsequently maintained through the combined action of cell-type specific transcription factors and broadly expressed regulatory machinery. Here, we provide a reference map of mouse development through gastrulation and early organogenesis, which can be used to explore the partitioning of early lineages and discrete cell states. Single-cell RNAseq data was collected on whole early mouse embryos. Each experiment consists of 4-10 replicates of developmental stages 6.5, 7.0, 7.5, 8.0, 8.5 for wild-type sequenced with 10X Genomics single-cell RNA sequencing system.