DataSheet2_Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq.xlsx

It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM > 0 and TPM > 0, respectively. In this study, we investigated the extent to which the combination of these transcriptomic analysis methods makes it possible to achieve a high coverage of the transcriptome encoded by the genes of other human chromosomes. A comparative analysis of transcriptome coverage for various types of biological material was carried out, and the HepG2 cell line transcriptome was compared with the transcriptome of liver tissue cells. In addition, the contribution of variability in the coverage of expressed genes in human transcriptomes to the creation of a draft human transcriptome was evaluated. For human liver tissues, ONT makes an extremely insignificant contribution to the overall coverage of the transcriptome. Thus, to ensure maximum coverage of the liver tissue transcriptome, it is sufficient to apply only one technology: Illumina RNA-Seq (FPKM > 0).

已有研究证实，当分别以FPKM>0与TPM>0作为截断阈值时，联合使用Illumina RNA测序（Illumina RNA-Seq）与牛津纳米孔技术（Oxford Nanopore Technologies, ONT）两种测序平台，可实现单条染色体——18号染色体——所编码基因对应的HepG2细胞系转录组的最优覆盖。本研究旨在探究这类转录组分析方法的联合应用，可在多大程度上实现人类其余染色体所编码基因的转录组的高覆盖度。研究团队针对多种生物材料开展了转录组覆盖度的比较分析，并将HepG2细胞系的转录组与肝脏组织细胞的转录组进行了对比。此外，本研究还评估了人类转录组中表达基因的覆盖度变异，对人类转录组草图构建的贡献水平。针对人类肝脏组织样本，牛津纳米孔技术（ONT）对转录组整体覆盖度的贡献微乎其微。因此，若要实现肝脏组织转录组的最大覆盖度，仅需采用单一技术：Illumina RNA-Seq（FPKM>0）即可。