RNA Detection

Contents

Preface..................................................................... v
Contributors................................................................ xi

1 The Secret Life of RNA: Lessons from Emerging Methodologies............. 1

Caroline Medioni and Florence Besse

2 Quantification of 2^0 - O-Me Residues in RNA Using Next-Generation

Sequencing (Illumina RiboMethSeq Protocol).............................. 29

Lilia Ayadi, Yuri Motorin, and Virginie Marchand

3 Identifying the m^6 A Methylome by Affinity Purification and Sequencing...... 49

Phillip J. Hsu and Chuan He

4 PARIS: Psoralen Analysis of RNA Interactions and Structures

with High Throughput and Resolution.................................... 59

Zhipeng Lu, Jing Gong, and Qiangfeng Cliff Zhang

5 Axon-TRAP-RiboTag: Affinity Purification of Translated mRNAs

from Neuronal Axons in Mouse In Vivo................................... 85

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.. ..................................................... 95

Susanne Nichterwitz, Julio Aguila Benitez, Rein Hoogstraaten,

Qiaolin Deng, and Eva Hedlund

7 Spatial Transcriptomics: Constructing a Single-Cell Resolution

Transcriptome-Wide Expression Atlas..................................... 111

Kaia Achim, Hernando Martı ́nez Vergara, and Jean-Baptiste Pettit

8 Single mRNA Molecule Detection inDrosophila............................ 127

Shawn C. Little and Thomas Gregor

9 Detection and Automated Analysis of Single Transcripts at Subcellular

Resolution in Zebrafish Embryos......................................... 143

L. Carine Stapel, Coleman Broaddus, and Nadine L. Vastenhouw

10 Super-Resolution Single Molecule FISH at theDrosophila
Neuromuscular Junction................................................. 163
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. ..................................................... 177
Catherine Rabouille

12 Hybridization Chain Reaction for Direct mRNA Detection
Without Nucleic Acid Purification.. ...................................... 187
Yao Xu and Zhi Zheng

vii