Extended Data Fig. 5: Integration of datasets spanning E3.5 to E13.5 of mouse development.

a, The number of cells per stage obtained from three previous studies^2,9,10, new E8.5 data obtained via optimized sci-RNA-seq3, and deeper sequencing of Cao et al.⁴. b, The number of cells per embryo corresponding to specific somite counts from new E8.5 data. c, Box plot of log2(UMI counts) per cell across the stages and studies (n = 1,658,968 cells).The center lines show the medians; the box limits indicate the 25th and 75th percentiles; the whiskers extend to the 5th and 95th percentiles; the outliers are represented by the dots. d, The same strategy of creating the edges between adjacent time points was performed after randomly shuffling the cell-state annotations for cells within each time point, followed by repeating this process 1,000 times, resulting in a null distribution of edge weights. After permutation, less than 1% of potential edges are assigned weights greater than 0.2 (red line). e, To quantify the quality of the integration between adjacent time points, we focused on cells at the later time point assigned to annotations that were also present at the earlier time point. We then calculated the fraction of these cells’ ancestral k-nearest neighbors (in the global 3D UMAP co-embedding) that were assigned the identical annotation. The mean proportion for different values of k are reported in the histogram. Of note, the lower value of this metric for E8.5a-E9.5 (red label) than E8.5a-E8.5b or E8.5b-E9.5 provides quantitative support for our claim that the new E8.5b data improved integration across the E8.5 to E9.5 (Extended Data Fig. 2).