Gastrulation is a critical milestone of embryogenesis at which the primary germ layers are formed and the multipotent embryonic cells are allocated to the progenitors of tissue lineages within the germ layers. Analysis of the spatial transcriptome of the post-implantation mouse embryos has revealed the dynamics of transcriptional and signalling activity in the germ layers and the transition of pluripotency state of the epiblast cell population. The activity of the regulon and signalling pathway underpinned the acquisition of lineage potency culminating in the generation of lineage-restricted germ layer progenitors and the tissue precursors of major body parts in the germ layers during gastrulation. The transcriptome further identifies the networks of molecular determinants that drive the allocation of embryonic cells to different tissue types and the regionalized genetic and signalling activity for building the basic body plan of the embryo. An important attribute of this knowledge is the translational application in stem cell biology for identifying and isolating precursor stem cells and directing the differentiation of stem cells to clinically relevant cell types for disease modelling and cellular therapy.