Extended Data Fig. 1: Integration of datasets generated by different groups using different scRNA-seq technologies.

a, As illustrated by a UMAP of coembedded E6.5 cells, batch effects are observed between three studies, as well as different embryos from the same study. The same UMAP is shown several times on the bottom of the panel, with colors highlighting cells from different studies or samples. b, UMAP of the same cells as in panel a with batch correction prior to integration¹³. The same UMAP is shown several times on the bottom of the panel, with colors highlighting cells from different studies or samples. In addition, the same UMAP is shown on the upper right, but colored by cell-type annotation. c, UMAP visualization of co-embedding of data from E8.5a (cells) generated on the 10x Genomics platform² and E9.5 (nuclei) generated using sci-RNA-seq3⁴, before batch correction¹³. The same UMAP is shown twice for both, with colors highlighting cells from either E8.5a (left) or E9.5 (right). E9.5 profiles were based on deeper sequencing of the same libraries reported in Cao et al.⁴. d, UMAP of the same cells as in panel c but with batch correction prior to integration¹³. Left and right as in panel c. ExE: extraembryonic. EmVE: embryonic visceral endoderm. ExVE: extraembryonic visceral endoderm.