MOESM2 of Recapitulation-like developmental transitions of chromatin accessibility in vertebrates

Additional file 2 Figure S1. Identification of conserved mid-embryonic stages during medaka embryogenesis by transcriptome similarity. Figure S2. Genomic distribution of mouse, chicken, and medaka ACRs with respect to genome annotations. Figure S3. Enhancers that drive wider expression tend to have higher ATAC-seq signals. Figure S4. Four methods for estimating evolutionary ages of ACRs. Figure S5. Categorization of evolutionary ages of ACRs and expressed protein-coding genes did not differ among different methods. Figure S6. The recapitulative pattern was also observed for relative sequence length of evolutionarily categorized ACRs within the genome. Figure S7. Developmental gene expression levels did not show a recapitulative pattern in the analysis including genes lost secondarily, related to Fig. 4. Figure S8. The recapitulative pattern of whole-embryo chromatin accessibility was consistent between methods I, II, III, and IV, related to Fig. 3. Figure S9. Essentially the same recapitulative pattern was observed in the analysis using different sets of species. Figure S10. Essentially the same recapitulative pattern was observed for the analyses with different criteria in filtering ATAC-seq reads. Figure S11. Chromatin accessibility of mouse early stages did not show the recapitulative pattern. Figure S12. Exonic ACRs did not follow a recapitulative pattern. Figure S13. Similar recapitulative pattern observed for the chromatin accessibility under strong negative selection. Figure S14. No ACR could be detected at three of five representative regulatory regions associated with taxon-specific features.