Single Cell Expression Profiling Resolves the Transcriptional Programs of Early Mesoderm Diversification

We analyzed 1,205 cells from the epiblast and nascent mesoderm of gastrulating mouse embryos by single cell RNA-seq, representing the first transcriptome-wide in vivo view of mammalian gastrulation. Based on the distribution of key marker genes and their spatiotemporal expression patterns within the embryo, we identified 10 cell clusters corresponding to the epiblast and developing mesodermal populations. This enabled us to explore the global gene expression dynamics associated with the induction of Brachyury, anterior-posterior patterning of the primitive streak and the earliest stages of blood development. Examination of Gata1 binding in Runx1-ires-GFP+/Gata1-mCherry+ (primitive erythroid) cells derived from 5 days of differentiation of ESCs towards haematopoietic cells