Additional file 1 of Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis

Additional file 1: Table S1. Hi-C library stats of CFM and CAM. Table S2. RNA-seq library stats of CFM and CAM. Table S3. Gene expression levels in CFM and CAM. Table S4. The first principal component (PC1) values of CFM and CAM at 1 Mb resolution. Table S5. The locations of topologically associated domains (TADs) of CFM and CAM at 40 kb resolution. Table S6. Stage-specific TAD boundaries of CFM and CAM at 40 kb resolution. Table S7. Loop list of CFM and CAM after merging loops at 5 kb and 10 kb resolutions. Table S8. ATAC-seq library stats of CFM and CAM. Table S9. Individual peak sets of four ATAC-seq samples. Table S10. Differentially accessible regions (DARs) between CFM and CAM. Table S11. Motif enrichment analysis of the differentially accessible regions (DARs). Table S12. Potential enhancers predicted by PSYCHIC at 25 kb resolution (FDR q-value < 0.05). Table S13. Landscape of cis-regulatory elements of cattle muscle genome based on ATAC-seq. Table S14. Stage-specific loops of cattle muscle. Table S15. E-P interactions involved in stage-specific loops. Table S16. Gene Ontology (GO) analysis of E-P genes in stage-specific loops using Metascape. Table S17. Motif enrichment analysis of E-P enhancers in stage-specific loops. Table S18. SRA ID of cattle used for selection sweep analysis. Table S19. Selection sweep signals (regions with ZFST > 3 were used for further analyses). Table S20. Genes and regulatory elements within sweep regions (ZFST > 3). Table S21. Fit-Hi-C loops (loops with FDR q-value < 0.05 were used for Fig. 5A). Table S22. Raw data of Dual-Luciferase reporter assay and PBM proliferation assay. Table S23. Primer sequences used in this study.