Part I: Bioinformatics
1. Introduction to Bioinformatics Resources for Post-Transcriptional Regulation of Gene Expression
Eliana Destefanis and Erik Dassi
2. Predicting RNA Secondary Structure Using In Vitro and In Vivo Data
Riccardo Delli Ponti and Gian Gaetano Tartaglia
3. RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment
Inbal Paz, Amir Argoetti, Noa Cohen, Niv Even, and Yael Mandel-Gutfreund
Part II: Expression Studies
4. Analysis of mRNA Translation by Polysome Profiling
Anne Cammas, Pauline Herviou, Le鮞a Dumas, and Stefania Millevoi
5. Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling
Alexander L. Cope, Sangeevan Vellappan, John S. Favate, Kyle S. Skalenko, Srujana S. Yadavalli, and Premal Shah
6. Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq
Sahil Sharma and Cynthia M. Sharma
7. Rapidly Characterizing CRISPR-Cas13 Nucleases Using Cell-Free Transcription-Translation Systems
Katharina G. Wandera and Chase L. Beisel
Part III: Interactomics
8. Studying RNP Composition with RIP
Annalisa Rossi and Alberto Inga
9. PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites
Charles Danan, Sudhir Manickavel, and Markus Hafner
10. A Pipeline for Analyzing eCLIP and iCLIP Data with htseq-clip and DEWSeq
Sudeep Sahadevan, Thileepan Sekaran, and Thomas Schwarz
11. Identification of miRNAs Bound to an RNA of Interest by MicroRNA Capture Affinity Technology (miR-CATCH)
Andrea Zeni, Margherita Grasso, and Michela A. Denti
12. Identifying the Protein Interactomes of Target RNAs Using HyPR-MS
Katherine B. Henke, Rachel M. Miller, Rachel A. Knoener, Mark Scalf, Michele Spiniello, and Lloyd M. Smith
Part IV: The RNA Lifecycle
13. Visualization and Quantification of Subcellular RNA Localization Using Single Molecule RNA Fluorescence In Situ Hybridization
Ankita Arora, Raeann Goering, Pedro Tirado Velez, and J. Matthew Taliaferro
14. Single-Molecule RNA Imaging Using Mango II Arrays
Adam D. Cawte, Haruki Iino, Peter J. Unrau, and David S. Rueda
15. Genome-Wide Identification of Polyadenylation Dynamics with TED-Seq
Yeonui Kwak and Hojoong Kwa
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