Doctoral thesis-Mengqi Wang-Chapter 3

<strong>Supplemental Table S1</strong> Detail information on cows selected for whole genome DNA methylation sequencing. <strong>Supplemental Table S2</strong> General statistics on whole genome DNA methylation sequencing read statistics <strong>Supplemental Table S3</strong> Comparisons of methylation level between cows with <em>S. aureus </em>subclinical mastitis and healthy control cows at a scope of the whole genome, chromosomes and gene features. <strong>Supplemental Table S4</strong> List of differentially methylated cytosines in the context of CpG <strong>Supplemental Table S5</strong> List of differentially methylated cytosines in the context of CHG and CHH <strong>Supplemental Table S6</strong> Distribution of differentially methylated cytosines among chromosomes and genetic features <strong>Supplemental Table S7</strong> Count of differentially methylated cytosines (DMCs) in the context of CpG, CHG and CHH in different gene features per gene <strong>Supplemental Table S8</strong> Functional enrichment of differentially expressed genes harboring differentially methylated cytosines at different genomic functional regions <strong>Supplemental Table S9</strong> Predicted methylation level for LINE-1 and tRNA-derived SINEs and comparisons between cows with <em>S. aureus </em>subclinical mastitis and healthy control cows <strong>Supplemental Table S10</strong> Differential methylation haplotype blocks and their colocation with QTLs related to mastitis and immune capacity <strong>Supplemental Table S11</strong> Differential genes with significant changes in general methylation level of regulatory regions and gene expression changes <strong>Supplemental Table S12</strong> Functional enrichment for differential genes with significant changes in general methylation level of regulatory regions and gene expression changes <strong>Supplemental Table S13</strong> Correlation between dMHBs located at regulatory regions and their overlapped differentially expressed genes <strong>Supplemental Table S14</strong> Motif enrichment and identification in GE-dMHBs <strong>Supplemental Table S15</strong> Functional enrichment for GE-dMHBs (dMHBs overlapped with genes and significantly correlated with the expression of corresponding genes) <strong>Supplemental Table S16</strong> Candidate discriminate signatures selected from GE-dMHBs (pro-GE-dMHBs) and their overlapped genes <strong>Supplemental Table S17</strong> Information about samples and primers used for TBAS and results of seven GE-dMHBs analyzed in 200 cows