Extended Data Figure 9: Cell cluster assignment is similar using either enhancer or gene tissue activity.

For each time point, cell clusters were annotated by first dividing peaks into TSS-distal (putative enhancers) and TSS-proximal (gene promoters) peaks. Each cell cluster was then annotated separately by overlaps between cluster-enriched peaks and: (1) enhancers, comparing the TSS-distal elements to the tissue or cell-type activity of characterized enhancers; (2) genes, comparing TSS-proximal elements to the tissue expression of genes; and (3) Gene Ontology (GO) information (see Methods). Shown are the cluster assignments based on enhancer, gene expression, or Gene Ontology annotation alone. The final assignment, used in the main figures, combines all enrichment information to produce more robust assignments.