Extended Data Fig. 3: Lineage progression.

a, UMAP plot as shown in Fig. 1c, coloured by the density of each cell in gene expression space; brighter coloured regions (towards yellow) are more densely sampled and darker regions (towards blue) are more sparsely sampled, relative to other regions in the atlas. Values shown are log₂(density + 1). b, Box plots summarizing the density per cell type. Values shown are log₂(density + 1). c, UMAP plots as shown in Fig. 1c, highlighting cells from each sampled time point and therefore illustrating the transcriptional progression along developmental time. d, Results of atlas stability testing (see Methods). y axis: ratio of the standard deviation of cell-type frequency to the mean cell-type frequency at different degrees of downsampling. Note that when the atlas is downsampled to less than half of its full size (50,000 cells), the standard deviation remains less than 10% of the mean for all cell types. x-axis is log-transformed. e, f, Abstracted graphs, which quantify the degree of similarity between the identified clusters to represent the underlying biological structure of the dataset. Nodes correspond to the annotated cell types, and edges reflect the confidence of adjacency between clusters (thicker edges indicate higher confidence). Node sizes increase as a function of the number of cells within each cluster. Nodes in e are coloured and numbered according to the legend shown in Fig. 1c. Nodes in f show the frequency of cells from each time point, excluding two samples of mixed time-point embryos.