Extended Data Fig. 1: Developmental expression of EcR-pathway TFs and bulk ATAC-Seq data.

a, Images showing immunostaining for EcR-B1, EcR-A, Hr3 and Ftz-f1 at the indicated time points. Scale bar, 50μm. Note: EcR-A positive cells at 36hAPF are glia. b, Comparison of replicates of bulk RNA-Seq of L1 neurons at 40hAPF, 60hAPF and 72hAPF. Values given are Spearman correlation values (see Methods). c, Coverage tracks from L1 bulk RNA-Seq in the EcR locus at 40hAPF, 60hAPF and 72hAPF. EcR-A, EcR-B1 and EcR-B2 transcripts are shown, and EcR-B1 specific exon is highlighted. d, Comparison of replicates of bulk ATAC-Seq data of L1 neurons at 40hAPF, 60hAPF and 72hAPF. Values shown are Spearman correlation values (see Methods). e, Comparison of change of ATAC-seq peak coverage (for regions with dynamic coverage over time) and change in expression of nearest gene. log₂(fold change RPKM of nearest gene) vs log₂(fold change ATAC-seq peak coverage) between 40hAPF and 60hAPF, and 60hAPF and 72hAPF. r, Pearson’s correlation coefficient. f, Distribution of the top 5000 peaks at each time point between various genomic landmarks. g, p-values (two-sided Hypergeometric test) for enrichment of binding motifs of EcR-usp complex, Hr3 and Nr5a1 (mammalian homolog for Ftz-f1) amongst the following sets of ATAC-Seq peaks: peaks going down from 40hAPF to 60hAPF, peaks going up from 40hAPF to 60hAPF, peaks going down from 60hAPF to 72hAPF, peaks going up from 60hAPF to 72hAPF, and peaks invariant over time. Red: occurrence of motif is higher than expected by chance, blue: occurrence of motif is lower than expected by chance (see Methods).