Supplementary tables for the manuscript titled "DNA methylation haplotype block signatures responding to S. aureus subclinical mastitis and association with production and health traits".

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

补充表S1：入选全基因组DNA甲基化测序的奶牛详细信息
补充表S2：全基因组DNA甲基化测序读段统计概要
补充表S3：全基因组、染色体及基因特征层面下，金黄色葡萄球菌（S. aureus）亚临床乳腺炎奶牛与健康对照奶牛的甲基化水平对比
补充表S4：CpG背景下的差异甲基化胞嘧啶（DMCs）列表
补充表S5：CHG与CHH背景下的差异甲基化胞嘧啶列表
补充表S6：差异甲基化胞嘧啶在染色体与遗传特征中的分布情况
补充表S7：各基因在不同基因特征中，CpG、CHG及CHH背景下的差异甲基化胞嘧啶数量统计
补充表S8：在不同基因组功能区域携带差异甲基化胞嘧啶的差异表达基因的功能富集分析结果
补充表S9：长散在核元件-1（LINE-1）与tRNA衍生短散在核元件（SINEs）的预测甲基化水平，以及金黄色葡萄球菌亚临床乳腺炎奶牛与健康对照奶牛的该指标对比
补充表S10：差异甲基化单倍型块（dMHBs）及其与乳腺炎、免疫能力相关数量性状位点（QTLs）的共定位情况
补充表S11：调控区域总甲基化水平发生显著改变且伴随基因表达变化的差异基因
补充表S12：调控区域总甲基化水平显著改变且伴随基因表达变化的差异基因的功能富集分析结果
补充表S13：位于调控区域的差异甲基化单倍型块（dMHBs）与其重叠的差异表达基因间的相关性
补充表S14：基因表达关联差异甲基化单倍型块（GE-dMHBs）中的基序富集与鉴定结果
补充表S15：基因表达关联差异甲基化单倍型块（GE-dMHBs，即与基因重叠且与对应基因表达显著相关的dMHBs）的功能富集分析结果
补充表S16：从基因表达关联差异甲基化单倍型块（GE-dMHBs，即pro-GE-dMHBs）中筛选得到的候选鉴别特征及其重叠基因
补充表S17：靶向亚硫酸氢盐扩增子测序（TBAS）所用样本与引物信息，以及200头奶牛中分析的7个GE-dMHBs的检测结果