RNA Modifications

Part I: Bioinformatic Tools to Study RNA Modifications

1. RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework
Ilaria Manfredonia and Danny Incarnato

2. An Informatics Pipeline for Profiling and Annotating RNA Modifications
Qi Liu, Xiaoqiang Lang, and Richard I. Gregory

Part II: Detecting RNA Modifications Using Nanopore Direct RNA Sequencing

3. EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing
Huanle Liu, Oguzhan Begik, and Eva Maria Novoa

4. Adaptation of Human Ribosomal RNA for Nanopore Sequencing of Canonical and Modified Nucleotides
Miten Jain, Hugh E. Olsen, Mark Akeson, and Robin Abu-Shumays

Part III: Next-Generation Sequencing Approaches to Detect and Capture Modified RNAs

5. AlkAniline-Seq: A Highly Sensitive and Specific Method for Simultaneous Mapping of 7-Methyl-Guanosine (m7G) and 3-Methyl-Cytidine (m3C) in RNAs by High-Throughput Sequencing
Virginie Marchand, Lilia Ayadi, Valérie Bourguignon-Igel, Mark Helm, and Yuri Motorin

6. Transcriptome-Wide Detection of Internal N7-Methylguanosine
Li-Sheng Zhang, Chang Liu, and Chuan He

7. miCLIP-MaPseq Identifies Substrates of Radical SAM RNA Methylating Enzyme Using Mechanistic Crosslinking and Mismatch Profiling
Vanja Stojkovi─ç, David E. Weinberg, and Danica Galoni─ç Fujimori

8. Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing
Bryan R. Cullen and Kevin Tsai

9. Quantitative and Single Nucleotide Resolution Profiling of RNA 5-Methylcytosine
Jun Li, Xingyu Wu, Trung Do, Vy Nguyen, Jing Zhao, Pei Qin Ng, Alice Burgess, Rakesh David, and Iain Searle

10. A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2''-O-Methyl RNAs
Erwin L. van Dijk and Claude Thermes

Part IV: Assessing RNA Modifications Using qPCR- and Molecular Biology-Based Methods

11. Assessing 2''-O-Methylation of mRNA Using Quantitative PCR
Brittany A. Elliott and Christopher L. Holley

12. Relative Quantification of Residue Specific m6A RNA Methylation Using m6A-RT-QPCR
Ane Olazagoitia-Garmendia and Ainara Castellanos-Rubio

13. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease
Jenna M. Lentini and Dragony Fu

14. Analysis of Queuosine tRNA Modifications Using APB Northern Blot Assays
Cansu Cirzi an