Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation

The blueprint of lineage segregation of early mouse embryo is established during gastrulation in which progenitors of various cell fates are regionalized and patterned in specific embryo locations. Despite the central importance of this period of mammalian development, we currently lack a comprehensive understanding of the underlying developmental trajectories and molecular processes, principally because research efforts either employed in vitro systems, focused on small numbers of genes, or limited the number of developmental stages or cell types that were studied. Here, we study the regulatory landscape of gastrulation by combining single-cell RNA-seq (A total of ~35,000 single cells isolated at E6.5, E6.75, E7.0, E7.25, E7.5) and geographical position sequencing (Geo-seq) technique, and we report a de novo identification of spatial signatures and a method to enable retrospective locating of single cells to their origins. Our work provides insights into the exit from pluripotency and priming for differentiation, and the emergence of regulatory networks associated with cell fate decisions. Finally, we reconstruct the spatio-temporal roadmap of gastrula mouse embryo in single-cell resolution. This result uncovers the cell migration trajectories and molecular processes associated with lineage segregation. Overall design: By using spatial transcriptome of Geo-seq , we carried out transcriptome profiling on embryo locations at a high resolution of 20-40 cells per sample. We then constructed a comprehensive spatio-temporal transcriptome map from the pre-gastrulation to late-gastrulation embryos. Combining single-cell RNA-seq data generated using 10x Genomics Chromium system, we visualized the spatio-temporal map in a 3D embryonic model. Definitions: region AP: region of 1st section of epiblast region EAP: region of 1st section of endoderm region Aregion of anterior epiblast/ectoderm region EP: region of posterior endoderm region P: region of posterior epiblast/ectoderm region EA: region of anterior endoderm region M: region of mesoderm region L: region of left lateral epiblast/ectoderm region R: region of right lateral epiblast/ectoderm region L1: region of left anterior lateral epiblast/ectoderm region L2: region of left posterior lateral epiblast/ectoderm region MA: region of anterior mesoderm region MP: region of posterior mesoderm region R1: region of right anterior lateral epiblast/ectoderm region R2: region of right posterior lateral epiblast/ectoderm region Epi: region of epiblast region VE: region of visceral endoderm region MAR: region of anterior right lateral mesoderm region MPL: region of posterior left lateral mesoderm region MPR: region of posterior right lateral mesoderm region MAL: region of anterior left lateral mesoderm