Extended Data Fig. 7: Estimated cell-type proportions for different regions of the gastrulating mouse embryo, arranged by inferred cell-type relationships over time.

a, The inferred cell–state proportions of each GEO-seq territory are robust to downsampling. For time point which GEO-seq data was available (E5.5, E6.0, E6.5, E7.0, and E7.5), we estimated a gene expression signature for each cell state from scRNA-seq data, either by using all the cells or by downsampling to a maximum of 50 cells per state, and then repeated the inference of cell-type contributors to each spatial territory of the gastrulating mouse embryo based on the application of CIBERSORTx to GEO-seq data^48,49. The Pearson correlation of resulting estimated cell–state proportions for each GEO-seq territory with downsampling (y-axes) or without downsampling (x-axes) are shown. Of note, we did not use downsampling in the results shown in Fig. 4b, As described in Fig. 4a, inference of cell-type contributor(s) to each spatial territory of the gastrulating mouse embryo based on the application of CIBERSORTx to GEO-seq data^48,49. As scRNA-seq data from E6.0 was unavailable, we used data from E6.25 instead. Black edges correspond to edges between cell states over time estimated by TOME (only edges with the largest weights are shown). In each corn plot, each circle or diamond refers to a GEO-seq sample, and its weighted color to the estimated cell-type composition. Corn plot nomenclature from Peng et al.⁴⁸. A, anterior; P, posterior; L, left lateral; R, right lateral; L1, anterior left lateral; R1, anterior right lateral; L2, posterior left lateral; R2, posterior right lateral; Epi1 and Epi2, divided epiblast; M, whole mesoderm; MA, anterior mesoderm; MP, posterior mesoderm; En1 and En2, divided endoderm; EA, anterior endoderm; EP, posterior endoderm.