Additional file 4 of Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism

Additional file 4: Table S11: The DNA methylation-sequenced reads and their mapping results in flesh callus. Table S12: The transcriptome-sequenced reads of flesh calli and their mapping results in pear. Table S13: The differentially expressed genes observed between the 5'-Aza-treated and control calli. Table S14: Identification of the DEGs modified by DNA methylation. Table S15: Integrative analysis of DAMs, DEGs, and DMRs. Table S16: Expression levels of methyltransferase, RdDM pathway, and demethylase genes in pear flesh at 11 stages. Table S17: The small RNA sequenced reads and their mapping results in pear flesh. Table S18: Correlation analysis of DAMs and cytosine methylation in the promoters of DEGs. Table S19: Correlation analysis of DAMs and DNA methylation in whole genome. Table S20: Isolation of the DNA methylation-modified DEGs correlated with the DAMs between two adjacent stages. Table S21: The expression patterns of all identified proteins in pear flesh. Table S22: Primers used in this study.

附加文件4：表S11：梨果肉愈伤组织的DNA甲基化测序读段（DNA methylation-sequenced reads）及其比对结果；表S12：梨果肉愈伤组织的转录组测序读段（transcriptome-sequenced reads）及其比对结果；表S13：5'-Aza处理组与对照组愈伤组织间的差异表达基因（differentially expressed genes, DEGs）；表S14：经DNA甲基化修饰的差异表达基因的鉴定；表S15：差异积累代谢物（differentially accumulated metabolites, DAMs）、差异表达基因（differentially expressed genes, DEGs）与差异甲基化区域（differentially methylated regions, DMRs）的整合分析；表S16：梨果肉11个发育阶段的甲基转移酶、RNA指导的DNA甲基化（RNA-directed DNA methylation, RdDM）通路及去甲基化酶基因的表达水平；表S17：梨果肉的小RNA测序读段（small RNA sequenced reads）及其比对结果；表S18：差异代谢物与差异表达基因启动子区域胞嘧啶甲基化的关联分析；表S19：差异代谢物与全基因组DNA甲基化的关联分析；表S20：相邻两个发育阶段间与差异代谢物相关的经DNA甲基化修饰的差异表达基因的筛选；表S21：梨果肉中所有鉴定得到的蛋白质的表达模式；表S22：本研究所用引物