Supplementary dataset for publication Effect of Pre-Weaning Nutrition on the Epigenetic and Transcriptomic Regulation of Mammary Gland Development in Holstein Heifer

Supplementary Information Table S1. Statistics on reads: Reads mapping statistics of RRBS data (A). Reads mapping statistics of RNA-seq data (B). Reads mapping statistics of miRNA-seq data (C). Table S2. Chromosomal distribution of DMSs in the context of CpG and the level of differences in their methylation in PAR tissue (A). The list of DMSs in different genetic regions identified in R vs AL comparisons (B). Functional enrichment of DM genes hypomethylated (C) and hypermethylated (D) in the AL group compared to the R group. Table S3. Chromosomal distribution of DMSs in the context of CpG and the level of differences in their methylation in MFP tissue (A). The list of DMSs in different genetic regions identified in R vs AL comparisons (B). Functional enrichment of DM genes hypomethylated (C) and hypermethylated (D) in the AL group compared to the R group. The enriched KEGG pathways involving genes with hypermethylated DMSs in fat pad tissue (E). Table S4. The list of differentially expressed miRNAs (DE miRNAs) identified in R vs AL comparisons in the PAR tissue (A). Functional enrichment of DE miRNA target genes in the AL group compared to the R group (B-D). The enriched KEGG pathways involving identified DEmiRNA target genes (E). Table S5. The list of differentially expressed miRNAs (DE miRNAs) identified in R vs AL comparisons in the MFP tissue (A). Functional enrichment of DE miRNA target genes in the AL group compared to the R group (B-D). The enriched KEGG pathways involving identified DE miRNA target genes (E). Table S6. The list of differentially expressed genes (DEGs) identified in R vs AL comparisons in the PAR tissue (A). Functional enrichment of upregulated (B) and downregulated (C) DEGs in the AL group compared to the R group. Table S7. The list of differentially expressed genes (DEGs) identified in R vs AL comparisons in the MFP tissue (A). Functional enrichment of upregulated (B,D,F) and downregulated (C,E,F) DEGs in the AL group compared to the R group (BP- biological processes; CC- cellular components, MF- molecular functions). The enriched KEGG pathways involving upregulated DEGs in fat pad tissue (H). Table S8. Functional enrichment of methylation-related DEGs in the MFP tissue (A-C) group (BP- biological processes; CC- cellular components, MF- molecular functions). The enriched KEGG pathways involving identified methylation-related DEGs (G). Table S9. Analysis of correlation between miRNA and target genes expression for all identified DE miRNAs and DEGs in the MFP tissue (A). Functional enrichment of DE miRNA-related DEGs (B-D). The enriched KEGG pathways involving identified DE miRNAs-related DEGs (E). Table S10. Primer sequences for validation of selected DEGs (A) and the results of validation of selected DEGs (B).