Description
Book SynopsisThis volume introduces different concepts and methods of detecting RNA in biological material in a variety of model systems.
Table of ContentsPreface…
Table of Contents…
Contributing Authors…
1. The Secret Life of RNA: Lessons from Emerging Methodologies
Caroline Medioni and Florence Besse
2. Quantification of 2'-O-Me Residues in RNA using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)
Lilia Ayadi, Yuri Motorin, and Virginie Marchand
3. Identifying the m6A Methylome by Affinity Purification and Sequencing
Phillip J. Hsu and Chuan He
4. PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution
Zhipeng Lu, Jing Gong, and Qiangfeng Cliff Zhang
5. Axon-TRAP-RiboTag: Affinity-Purification of Translated mRNAs from Neuronal Axons in Mouse In Vivo
Toshiaki Shigeoka, Jane Jung, Christine E. Holt, and Hosung Jung
6. LCM-Seq: A Method for Spatial Transcriptomic Profiling using Laser Capture Microdissection Coupled with PolyA-Based RNA Sequencing
Susanne Nichterwitz, Julio Aguila Benitez, Rein Hoogstraaten, Qiaolin Deng, and Eva Hedlund
7. Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas
Kaia Achim, Hernando Martínez Vergara, and Jean-Baptiste Pettit
8. Single mRNA Molecule Detection in Drosophila
Shawn C. Little and Thomas Gregor
9. Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos
L. Carine Stapel, Coleman Broaddus, and Nadine L. Vastenhouw
10. Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction
Joshua S. Titlow, Lu Yang, Richard M. Parton, Ana Palanca, and Ilan Davis
11. Detection of mRNA and Associated Molecules by ISH-IEM on Frozen Sections
Catherine Rabouille
12. Hybridization Chain Reaction for Direct mRNA Detection without Nucleic Acid Purification
Yao Xu and Zhi Zheng
13. In Situ Detection of MicroRNA Expression with RNAscope Probes
Viravuth P. Yin
14. Padlock Probes to Detect Single Nucleotide Polymorphisms
Tomasz Krzywkowski and Mats Nilsson
15. Quantifying Gene Expression in Living Cells with Ratiometric Bimolecular Beacons
Yantao Yang, Mingming Chen, Christopher K. Krueger, Andrew Tsourkas, and Antony K. Chen
16. Optimizing Molecular Beacons for Intracellular Analysis of RNA
Mingming Chen, Yantao Yang, Christopher K. Krueger, and Antony K. Chen
17. Live Imaging of Nuclear RNPs in Mammalian Complex Tissue with ECHO-liveFISH
Dan Ohtan Wang
18. In Vivo Visualization and Function Probing of Transport mRNPs using Injected FIT Probes
Jasmine Chamiolo, Imre Gaspar, Anne Ephrussi, and Oliver Seitz
19. Visualizing RNA in Live Bacterial Cells using Fluorophore- and Quencher-Binding AptamersMurat Sunbul, Ankita Arora, and Andres Jäschke
20. Method for Imaging Live-Cell RNA using an RNA Aptamer and a Fluorescent Probe
Shin-ichi Sato, Kenji Yatsuzuka, Yousuke Katsuda, and Motonari Uesugi
21. RNA Live Imaging in the Model Microorganism Ustilago maydis
S. Zander, K. Müntjes, and M. Feldbrügge
22. Real-Time Fluorescence Imaging of Single-Molecule Endogenous Non-Coding RNA in Living Cells
Hideaki Yoshimura and Takeaki Ozawa
23. Live Imaging of mRNA Synthesis in Drosophila
Hernan G. Garcia and Thomas Gregor
24. Imaging Newly Transcribed RNA in Cells by Using a Clickable Azide-Modified UTP Analog
Anupam A. Sawant, Sanjeev Galande, and Seergazhi G. Srivatsan
25. Detection of the First Round of Translation: The TRICK Assay
Franka Voigt, Jan Eglinger, and Jeffrey A. Chao
26. Imaging Translation Dynamics of Single mRNA Molecules in Live Cells
Suzan Ruijtenberg, Tim A. Hoek, Xiaowei Yan, and Marvin E. Tanenbaum
27. Systematic Detection of Poly(A)+ RNA-Interacting Proteins and Their Differential Binding
Miha Milek and Markus Landthaler
28. Isolation and Characterization of Endogenous RNPs from Brain Tissues
Rico Schieweck, Foong yee Ang, Renate Fritzsche, and Michael A. Kiebler
29. Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein-RNA Interactions
Christopher R. Sibley
30. RNA Tagging: Preparation of High-Throughput Sequencing Libraries
Christopher P. Lapointe and Marvin Wickens
31. RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells
Colleen A. McHugh and Mitchell Guttman
