Li Yanqiang, Chen Jiayi, Wang Yunxia, Li Dean, Li Jiahan, Yi Yang, Zhang Lili, Cao Qi, Chen Kaifu
Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
STAR Protoc. 2025 Jul 31;6(3):104003. doi: 10.1016/j.xpro.2025.104003.
2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. Here, we present an integrated bioinformatics protocol for the identification of 2'-O-methylation using nanopore direct RNA sequencing (RNA-seq) data. We describe steps for software installation, data collection, and training the machine learning model. We then detail procedures for mapping 2'-O-methylation in both rRNA and mRNA in yeast and human cells. For complete details on the use and execution of this protocol, please refer to Li et al..
2'-O-甲基化（Nm）在核糖体RNA（rRNA）和信使核糖核酸（mRNA）的内部位点中起着关键作用。在此，我们提出了一种综合生物信息学方案，用于利用纳米孔直接RNA测序（RNA-seq）数据鉴定2'-O-甲基化。我们描述了软件安装、数据收集以及训练机器学习模型的步骤。然后，我们详细介绍了在酵母和人类细胞的rRNA和mRNA中定位2'-O-甲基化的程序。有关本方案使用和执行的完整详细信息，请参考Li等人的研究。
