Fig. 2: A single-cell resolution 4D molecular atlas of mouse gastrulation.

a The pipeline of multi-dimension single-cell (MDSC) mapping. The SRCCs of the expression values of the zipcodes of each single cell against all reference samples of the reference embryo were calculated, followed by the application of a spatial smoothing algorithm to impute the high-confidence (closest) location (see “Methods”). The mapping of cells to position 8P was shown as an example. b Verification of the results of MDSC Mapping of single cells isolated from a known position in an E7.0 embryo. The number on each corn indicates the number of cells mapped to the Geo-seq position in the germ layers. PCC values and confidence intervals are shown for the simulation. c Uniform manifold approximation and projection (UMAP) plot showing the data structure of the “Gastrulation Atlas” comprising 32,940 cells from E6.5 to E7.5 embryos, with the exclusion of extraembryonic cells. Twenty-five cell types are annotated (see color legend). Def. endoderm definitive endoderm, PGC primordial germ cells. d Fraction of cell type per time point, displaying a progressive increase in cell-type complexity during gastrulation. e MDSC Mapping results of exemplar cell types for E6.5, E6.75, E7.0, E7.25, and E7.5 embryos. The number in each corn indicates the number of cells mapped to the specific Geo-seq position. f The spatiotemporal distribution of all the single cells identified in the Gastrulation Atlas of E6.5–E7.5 mouse embryos. Cell types are annotated as in (c). g The spatiotemporal distribution of single cells annotated as “nascent mesoderm” in the epiblast and mesoderm of E6.5–E7.5 embryos. h The spatio-temporal distribution of Pou3f1-expressing cells in E6.5–E7.5 embryos. The color legend indicates the level of expression determined by the transcript counts.