Extended Data Fig. 9: The annotations and dynamics of ZEPA cCREs.
a, Scatter plot showing the correlation between the number of cell types and the number of cCREs in each stage, colored by stages. b, Heatmap showing bases proportion of all candidate cCREs overlapping bulk ATAC-seq peaks in this study, bulk ATAC-seq peaks from 12 adult zebrafish tissues2, enhancers defined by Yang et al.2, or annotated transcriptional start sites50. c, Bar chart showing the ratio of the peaks overlapped with the quiescent state (10_Quies) in each stage. d, Pearson’s correlations of cCRE chromatin accessibility between single-cell and bulk ATAC-seq data across 20 developmental stages. e, Pearson’s correlations of cCREs chromatin accessibility between replicates from the same stage (that is, developmental stages separating data sets is 0), or from different stages separated by one to eleven intervening stages, as indicated. n = 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1 from left to right boxes, respectively. Boxes span the first to third quartiles (Q1 to Q3), the horizontal line denotes the median, and the whiskers show 1.5× the interquartile range (IQR). f, Genome browser tracks of chromatin accessibility profiles of bulk ATAC-seq at gad2, and myo3a loci. g, Gene Ontology and Zebrafish Wild-type Expression analysis for cCREs in the development-related cluster in Fig. 4j by GREAT60 ontology enrichment analysis with the binomial distribution test. h, Transcription factor motif enriched in each development-related cCREs cluster of Fig. 4j by using Homer with the one-sided hypergeometric distribution test. Source numerical data are provided as source data.
