Molecular architecture of lineage specification and tissue organization in early mouse embryo
Dataset ID: STDS0000077
23,361 Genes


Dataset information
During postimplantation development of the mouse embryo, descendants of the inner cell mass cells in the early epiblast transit from the naïve pluripotent state to the primed pluripotent state. Concurrent with the transition of the pluripotency states is the specification of cell lineages and formation of germ layers in the embryos that serves as the blueprint for embryogenesis. Fate mapping and lineage analysis studies have revealed that cells in different regions of the germ layers acquire location-specific cell fates during gastrulation. The regionalization of cell fates heralding the formation of the basic body plan is conserved in vertebrate embryos at a common phylotypic stage of development. Knowledge of the molecular regulation that underpin the lineage specification and tissue patterning is instrumental for understanding embryonic programming and stem cell-based translational study. However, a genome-wide molecular annotation of lineage segregation and tissue architecture of post-implantation embryo has yet to be undertaken. Here, we reported a spatially resolved transcriptome of cell populations at defined positions in the germ layers over the period of pre- to late gastrulation development. This spatio-temporal transcriptome provides high resolution digitized gene expression profiles and defines the molecular attribute of the genealogy of lineages and continuum of pluripotency states in time and space. The transcriptome further identifies the networks of molecular determinants that drive lineage specification and tissue patterning in the early postimplantation mouse embryo.
Overall design
By using spatial transcriptome of Geo-seq, we carried out transcriptome profiling on embryo sections at a high resolution of 20-40 cells per sample. We then constructed a comprehensive spatial transcriptome map from the pre-gastrulation to late-gastrulation embryos that are visualized in a 3D embryonic model based on the sequencing data. Please be aware that the positions for left (L) and right (R) are from mirrored images and should be considered as right and left in real embryo settings. Anterior (A) or Posterior (P) regions do not change.
Illumina HiSeq 2500, Illumina NovaSeq 6000
Mus musculus
Organ parts
Cell types
Mouse embryonic cells
Development stage
Pre-gastrulation embryo (E5.5), Pre-gastrulation embryo (E6.0), Early-gastrulation embryo (E6.5), Mid-gastrulation embryo (E7.0), Late-gastrulation embryo (E7.5)
Peng G, Suo S, Cui G, Yu F et al. Molecular architecture of lineage allocation and tissue organization in early mouse embryo. Nature 2019 Aug;572(7770):528-532
Submission date: 2018-10-09Update date: 2020-08-05

Guangdun Peng; Guizhong Cui; Shengbao Suo; Naihe Jing; Jing-Dong J Han

GEO Series Accessions: GSE120963