Extended Data Figure 10: sci-ATAC-seq can predict tissue-specific enhancer usage during development.

All candidate clade-specific enhancers tested in transgenic reporters. For each time point, upper panels show single cells visualized by t-SNE with the blue intensity representing the number of sci-ATAC-seq reads obtained from each tested element in each individual cell. Cell clusters bounded by dashed lines correspond to the predicted clade of activity. Lower panels show representative embryos for each time point with nuclei stained with DAPI (grey), in situ hybridization of the reporter gene driven by the enhancer (yellow) and a tissue marker (magenta). Annotation of each element’s activity involved observations across hundreds of embryos. Scale bar, 50 μm.