Additional file 2 of Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs

Additional file 2: Table S1. Statistics of the resequencing data produced by this study. Table S2. Overview of the data that were downloaded from NCBI. Table S3. Statistics of the NCBI data—according to run_ID. Table S4. Primers used in this study. Table S5. Information on the luciferase reporter assay for 10 selected potential enhancers. Table S6. siRNA sequences used in this study. Table S7. BioNano optical maps of the Luchuan pig. Table S8. Statistics of the two haplotigs in each step of assembly processes. Table S9. Size distribution of presence variations in Luchuan assembly compared with Sscrofa11.1 reference. Table S10. Predicted protein-coding genes located in the regions of Luchuan pig presence variations compared with the Sscrofa11.1 reference. Table S11. GO enrichment of genes in expanded and contracted families of Luchuan pig (qvalue < 0.05). Table S12. Statistics of the SNP dataset and Duroc genome. Table S13. Cross-validation error value. Table S14. Selected genes in eastern pig group. Table S15. Selected genes in western pig group. Table S16. (a) Enrichment pattern of genes under potential selection in pig GWAS regions; and (b) Enrichment pattern of genes under potential selection in pig QTL regions. Table S17. (a) Genes with selective signals, GWAS signals, and highly differential functional coding variants; and (b) Genes with refined selective signals and GWAS signals relevant to pig economic traits. Table S18. Information of LYZ promoter variants. Table S19. Information of the novel lncRNAs. Table S20. Differentially expressed genes between Luchuan and Duroc pigs in different tissues. Table S21. Statistics of differentially expressed genes including both mRNAs and lncRNAs. Table S22. Five types of differential isoform usage between Luchuan and Duroc in each tissue. Table S23. Enrichment of DEG promoters in highly differential variants under potential selection. Table S24. DEG that do not have highly differential functional coding but promoter variants under potential selection. Table S25. ATAC-seq reads and peaks of each sample. Table S26. GO enrichment of ATAC-seq peaks in different tissues. Table S27. Motif enrichment of ATAC-seq peaks in different tissues. Table S28. Enrichment of open chromatin regions with promoters excluded in highly differential variants under potential selection. Table S29. Significant enriched GO terms of differential ATAC-seq peaks. Table S30. (a) DEG associated with promoters with highly differential variants under potential selection; and (b) DEG associated with distal differential ATAC-seq peaks with highly differential variants. Table S31. Identification of putative functional lncRNAs in pig genome by integrative analysis. Table S32. Alternative splicing under selection in the ± 2 bp region of the relevant intron/exon junctions.