Extended Data Fig. 1. Integration and cell-type annotation.

a. Brightfield images of representative embryos isolated from 3 independent foster mice and staged for the respective developmental stages. Scale bar, 500 µm. b. Distribution of beads profiled by Slide-seq from the respective stages. c. Violin plots showing the number of UMIs or genes recovered per bead. Log₁₀ values are used to represent counts. UMI, unique molecular identifier. d. Violin plots showing the number of UMIs and genes recovered per bead across individual arrays. Log₁₀ values are used to represent counts. UMI, unique molecular identifier. e. Uniform Manifold Approximation and Projection (UMAP) of Slide-seq data and 10X scRNA-seq reference atlas of mouse gastrulation²⁶. The color of the beads corresponds to the predicted and annotated cell state. Inset: UMAP representation of beads covered by the indicated modalities (red). Each dot represents a bead or a cell. f. UMAP of integrated data from stages E6.5 to E9.5. Black beads represent cells/beads from the corresponding stage. Each dot represents a bead or a cell.