Alternative Splicing: Methods and Protocols

1. Alternative Splicing in Human Biology and Disease

Daniel Jutzi and Marc-David Ruepp

2. Targeting Alternative Splicing for Therapeutic Interventions

Jessica L. Centa and Michelle L. Hastings

3. An Optimized Protocol for the Mapping of Cell Type-Specific Ribosome-Associated Transcript Isoforms from Small Mouse Brain Regions

Giulia Di Bartolomei and Peter Scheiffele

4. FACS-Based Neuronal Cell Type-Specific RNA Isolation and Alternative Splicing Analysis

Zicheng Wei, Yuxin Qin, Gordon Fishell, and Boxing Li

5. Quantitative Measurement of Alternatively Spliced RNA Isoform Levels

Zhelin Jeff Li and Sika Zheng

6. Analysis of Splicing Regulation by Third-Generation Sequencing

7. Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework

Andr Gohr, Federica Mantica, Antonio Hermoso-Pulido, Javier Tapial, Yamile Mrquez, and Manuel Irimia

8. Identification and Quantification of Microexons Using Bulk and Single-Cell RNA-Seq Data

Guillermo E. Parada and Martin Hemberg

9. Functional Annotation of Custom Transcriptomes

Fursham Hamid, Kaur Alasoo, Jaak Vilo, and Eugene Makeyev

10. Design, Labeling, and Application of Probes for RNA smFISH

Ewa Piskadlo, Bastian Th. Eichenberger, Luca Giorgetti, and Jeffrey A. Chao

11. BaseScope(TM) Approach to Visualize Alternative Splice Variants in Tissue

Alexandra Bunda and Arturo Andrade

12. In Situ Imaging of mRNA Splicing Variants by SpliceRCA

Xiaojun Ren and Jinghong Li

13. Two-Color Fluorescent Reporters for Analysis of Alternative Splicing

John A. Calarco and Pallavi P. Pilaka

14. Quantitative Detection of Protein Splice Variants by Selected Reaction Monitoring (SRM) Mass Spectrometry

15. Probing the Interactions of Splicing Regulatory Small Molecules and Proteins with U1 snRNP Using NMR Spectroscopy

Sbastien Campagne, Tebbe de Vries, and Frdric H-T. Allain

16. Genome-Wide CRISPR Screening to Identify Mammalian Factors that Regulate Intron Retention

Anna M. Scarborough, Ashwin Govindan, and Nicholas K. Conrad

17. Tethered Function Assays to Elucidate the Role of RNA-Binding Proteins