Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm
Summary: 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, a...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-09-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725004095 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849415238264291328 |
|---|---|
| author | Yanqiang Li Jiayi Chen Yunxia Wang Dean Li Jiahan Li Yang Yi Lili Zhang Qi Cao Kaifu Chen |
| author_facet | Yanqiang Li Jiayi Chen Yunxia Wang Dean Li Jiahan Li Yang Yi Lili Zhang Qi Cao Kaifu Chen |
| author_sort | Yanqiang Li |
| collection | DOAJ |
| description | Summary: 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.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-b6f0b1fcf2d94f24bedbe27748e50af2 |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-b6f0b1fcf2d94f24bedbe27748e50af22025-08-20T03:33:35ZengElsevierSTAR Protocols2666-16672025-09-016310400310.1016/j.xpro.2025.104003Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNmYanqiang Li0Jiayi Chen1Yunxia Wang2Dean Li3Jiahan Li4Yang Yi5Lili Zhang6Qi Cao7Kaifu Chen8Basic 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; Corresponding authorBasic 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, USABasic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USABasic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USABasic 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; Commonwealth School, Boston, MA 02116, USADepartment of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USABasic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USADepartment of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USABasic 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; Broad Institute of MIT and Harvard, Boston, MA 02215, USA; Dana-Farber/Harvard Cancer Center, Boston, MA 02215, USA; Corresponding authorSummary: 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.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725004095BioinformaticsGenomicsRNA-seq |
| spellingShingle | Yanqiang Li Jiayi Chen Yunxia Wang Dean Li Jiahan Li Yang Yi Lili Zhang Qi Cao Kaifu Chen Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm STAR Protocols Bioinformatics Genomics RNA-seq |
| title | Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm |
| title_full | Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm |
| title_fullStr | Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm |
| title_full_unstemmed | Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm |
| title_short | Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm |
| title_sort | protocol for mapping 2 o methylation using nanopore direct rna seq data with nanonm |
| topic | Bioinformatics Genomics RNA-seq |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725004095 |
| work_keys_str_mv | AT yanqiangli protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm AT jiayichen protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm AT yunxiawang protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm AT deanli protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm AT jiahanli protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm AT yangyi protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm AT lilizhang protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm AT qicao protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm AT kaifuchen protocolformapping2omethylationusingnanoporedirectrnaseqdatawithnanonm |