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

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, Valrie 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 Stojkovic, David E. Weinberg, and Danica Galonic 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 and