PDF(Pubmed)
Abstract：
Introduction: We have previously observed phenotypic and developmental changes upon the ectopic expression of the RUNX3 or the ZBTB46 transcription factors in mouse embryonic stem cell (ESC) derived progenitors. In this study, we evaluated the gene expression profiles of the RUNX3- and the ZBTB46-instructed murine ESCs with RNA-seq testing two next-generation sequencing technologies. Methods: We compared the DNA nanoball-based DNBSEQ G400 sequencer (MGI) with the bridge-PCR-based NextSeq 500 instrument (Illumina) for RNA sequencing. Moreover, we also compared two types of MGI sequencing reagents (Standard versus Hot-massive parallel sequencing (MPS)) with the DNBSEQ G400. Results: We observed that both sequencing platforms showed comparable levels of quality, sequencing uniformity, and gene expression profiles. For example, highly overlapping RUNX3- and ZBTB46-regulated gene lists were obtained from both sequencing datasets. Moreover, we observed that the Standard and the Hot-MPS-derived RUNX3- and ZBTB46-regulated gene lists were also considerably overlapped. This transcriptome analysis also helped us to identify differently expressed genes in the presence of the transgenic RUNX3 or ZBTB46. For example, we found that Gzmb, Gzmd, Gzme, Gdf6, and Ccr7 genes were robustly upregulated upon the forced expression of Runx3; on the other hand, Gpx2, Tdpoz4, and Arg2 were induced alongside the ectopic expression of Zbtb46. Discussion: Similar gene expression profile and greatly overlapping RUNX3- and ZBTB46-regulated gene sets were detected with both DNA sequencing platforms. Our analyses demonstrate that both sequencing technologies are suitable for transcriptome profiling and target gene selection. These findings suggest that DNBSEQ G400 represents a cost-effective alternative sequencing platform for gene expression monitoring. Moreover, this analysis provides a resource for exploration of the RUNX3- and ZBTB46-dependent gene regulatory networks.
摘要：
简介：我们以前已经观察到RUNX3或ZBTB46转录因子在小鼠胚胎干细胞（ESC）来源的祖细胞中异位表达时的表型和发育变化。在这项研究中,我们使用RNA-seq测试两种下一代测序技术,评估了RUNX3-和ZBTB46指导的鼠ESC的基因表达谱.方法：我们比较了基于DNA纳米球的DNBSEQG400测序仪（MGI）与基于桥PCR的NextSeq500仪器（Illumina）进行RNA测序。此外，我们还比较了两种类型的MGI测序试剂(标准与热大规模平行测序(MPS))与DNBSEQG400。结果：我们观察到两个测序平台均显示出可比的质量水平，测序均匀性,和基因表达谱。例如,从两个测序数据集获得了高度重叠的RUNX3-和ZBTB46调控的基因列表.此外，我们观察到标准品和Hot-MPS衍生的RUNX3-和ZBTB46调节的基因列表也有相当大的重叠。该转录组分析还帮助我们在转基因RUNX3或ZBTB46的存在下鉴定不同表达的基因。例如,我们发现Gzmb,Gzmd,Gzme,Gdf6和Ccr7基因在Runx3的强制表达后被强烈上调；另一方面，Gpx2、Tdpoz4和Arg2与Zbtb46的异位表达一起被诱导。讨论:用两种DNA测序平台检测到相似的基因表达谱和极大重叠的RUNX3和ZBTB46调节的基因集。我们的分析表明，两种测序技术都适用于转录组分析和靶基因选择。这些发现表明DNBSEQG400代表了用于基因表达监测的成本有效的替代测序平台。此外，本分析为探索依赖RUNX3和ZBTB46的基因调控网络提供了资源.
