1. 5'bromouridine IP Chase (BRIC)-Seq to Determine RNA Half Lives
Toshimichi Yamada, Naoto Imamachi, Rena Mizutani, Katsutoshi Imamura, Yutaka Suzuki, and Nobuyoshi Akimitsu
2. Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq)
Farah Abdul-Rahman and David Gresham
3. Metabolic Labeling of Newly Synthesized RNA with 4sU to in Parallel Assess RNA Transcription and Decay
Wei Sun and Wei Chen
4. Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH
Tatjana Trcek, Samir Rahman, and Daniel Zenklusen
5. PAR-CLIP for Discovering Target Sites of RNA-Binding Proteins
Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer, and Thomas Tuschl
6. Characterizing mRNA Sequence Motifs in the 3'UTR Using GFP Reporter Constructs
Rene Geissler and Andrew Grimson
7. iCLIP of the PIWI Protein Aubergine in Drosophila Embryos
Bridlin Barckmann, Jérémy Dufourt, and Martine Simonelig
8. Integration of ENCODE RNAseq and eCLIP Data Sets
Jorge Boucas
9. Identifying miRNA Targets Using AgoRIP-Seq
Rebecca Petri and Johan Jakobsson
10. Integrated Analysis of miRNA and mRNA Expression Profiles to Identify miRNA Targets
Zhiming Li and Chi-Meng Tzeng
11. Identifying RISC Components Using Ago2 Immunoprecipitation and Mass Spectrometry
Tingfang Yi
12. Using Tet-Off Cells and RNAi Knockdown to Assay mRNA Decay
Thomas D. Baird and J. Robert Hogg
13. Identifying Cellular Nonsense-Mediated mRNA Decay (NMD) Targets: Immunoprecipitation of Phosphorylated UPF1 Followed by RNA Sequencing (p-UPF1 RIP-Seq)
Tatsuaki Kurosaki, Mainul Hoque, and Lynne E. Maquat
14. Generation of Cell Lines Stably Expressing a Fluorescent Reporter of Nonsense-Mediated mRNA Decay Activity
Nadezhda M. Markina, Anton P. Pereverzev, Dmitry B. Staroverov, Konstantin A. Lukyanov, and Nadya G. Gurskaya
15. Reactivation Assay to Identify Direct Targets of the Nonsense-Mediated mRNA Decay Pathway in Drosophila
Jonathan O. Nelson and Mark M. Metzstein
16. Studying Nonsense-Mediated mRNA Decay in Mammalian Cells Using a Multicolored Bioluminescence-Based Reporter System
Andrew Nickless and Zhongsheng You
