Additional file 2 of Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns

Additional file 2: Table S1A. Sample information for the WGBS; Table S1B. Sample information for the RNA sequencing; Table S1C. Sample information for the whole genome sequencing; Table S2. Comparison of methylation statistics between two different cattle reference assemblies. Table S3. DMC and DMR number for each comparison pairs. Please note that the numbers, which may be affected by different common data amount for each tissue. Table S4. PMD information for different samples. Table S5. Placenta PMD percentages and genes located in the shared and lineage-specific placenta PMDs between cattle and human. Table S6. GO analyses for genes shared or specific in PMDs between human placenta and cattle placenta. Table S7. Gene ontology analysis for genes overlapping with cattle placenta HMD. Table S8. GO analysis for the genes overlapped with cattle placenta PMDs. Table S9. Information of 16 non-blood DNA methylation level drops. Table S10. Differentially methylated TSS-HMR between human and cattle. Table S11. Gene ontology analysis for genes totally located in the HMR. Table S12. common twin genes in one HMR core region between cattle and human. Table S13. Gene ontology analyses for genes specifically high expressed in different tissues. Table S14. Information for experimentally supported CpG Islands.

附加文件2：表S1A为全基因组亚硫酸氢盐测序（Whole Genome Bisulfite Sequencing, WGBS）样本信息；表S1B为RNA测序（RNA sequencing）样本信息；表S1C为全基因组测序（Whole Genome Sequencing, WGS）样本信息。表S2：两种不同牛参考基因组组装版本的甲基化统计量对比。表S3：各比对组的差异甲基化胞嘧啶（Differentially Methylated Cytosine, DMC）与差异甲基化区域（Differentially Methylated Region, DMR）数量。请注意：该数值可能受不同组织的测序数据量差异影响。表S4：不同样本的部分甲基化区域（Partially Methylated Domain, PMD）信息。表S5：牛与人类共有的以及谱系特异性胎盘PMD的胎盘PMD占比，以及位于这些区域内的基因信息。表S6：人类胎盘与牛胎盘PMD中共有或特异性基因的基因本体（Gene Ontology, GO）分析结果。表S7：与牛胎盘高甲基化区域（Hypermethylated Domain, HMD）重叠的基因的GO分析结果。表S8：与牛胎盘PMD重叠的基因的GO分析结果。表S9：16例非血液样本的DNA甲基化水平下降相关信息。表S10：人类与牛之间的差异甲基化TSS-HMR（转录起始位点-低甲基化区域，Transcription Start Site-Hypomethylated Region）信息。表S11：完全位于HMR内的基因的GO分析结果。表S12：牛与人类共有的某一HMR核心区域内的共有孪生基因信息。表S13：不同组织特异性高表达基因的GO分析结果。表S14：实验验证的CpG岛（CpG Island）相关信息。