Features samples for subsequent analysis by high-throughput technologies, such as deep sequencing or microarray analysis -Contains thorough, detailed methods and protocols easily implemented by novices and experts alike -Includes vital shared expert knowledge in the form of notes on avoiding potential experimental pitfalls

Part I: RNA Methods

1. The Transcriptional Landscape
Henrik Nielsen

2. Working with RNA
Henrik Nielsen

3. Synthesis of RNA by In vitro Transcription
Bertrand Beckert and Benoit Masquida

4. Efficient Poly(A)+ RNA Selection Using LNA Oligo(T) Capture
Nana Jacobsen, Jens Eriksen, and Peter Stein Nielsen

5. Genome Browsers
Elfar Torarinsson

6. Web-Based Tools for Studying RNA Structure and Function
Ajish D. George and Scott A. Tenenbaum

7. Northern Blotting Analysis
Knud Josefsen and Henrik Nielsen

8. Rapid Amplification of cDNA Ends (RACE)
Oladapo Yeku and Michael A. Frohman

9. Fractionation of mRNA Based on the Length of the Poly(A) Tail
Hedda A. Meijer and Cornelia H. de Moor

10. Analysis of Mutations that Influence Pre-mRNA Splicing
Zhaiyi Zhang and Stefan Stamm

11. S1 Nuclease Analysis of Alternatively Spliced mRNA
Martin Lützelberger and Jørgen Kjems

12. Promises and Challenges in Developing RNAi as a Research Tool and Therapy
Mouldy Sioud

13. Inhibition of Gene Function in Mammalian Cells Using Short-Hairpin RNA (shRNA)
Jørn Remi Henriksen, Jochen Buechner, Cecilie Løkke, Trond Flægstad, and Christer Einvik

14. Validation of RNAi by Real Time PCR
Knud Josefsen and Ying C. Lee

15. Profiling RNA Polymerase II Using the Fast Chromatin Immunoprecipitation Method
Joel Nelson, Oleg Denisenko, and Karol Bomsztyk

Part II: RNP Methods

16. The Post-Transcriptional Operon
Scott A. Tenenbaum, Jan Christiansen, and Henrik Nielsen

17. RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling
Ritu Jain, Tiffany Devine, Ajish D. George, Sridar V. Chittur, Timothy E. Baroni, Luiz O. Penalva, and Scott A. Tenenbaum

18. Isolation of RNP Granules
Lars Jønson, Finn Cilius Nielsen, and Jan Christiansen

19. Electrophoretic Mobility Shift Assay for Characterizing RNA-Protein Interaction
Keith T. Gagnon and E. Stuart Maxwell

20. Polysome Analysis and RNA Purification from Sucrose Gradients
TomᚠMašek, Leoš Valášek, and Martin Pospíšek

21. Prediction of Targets for microRNAs
Morten Lindow

22. Outsourcing of Experimental Work
Henrik Nielsen

Also features electronic supplemental chapters:

ESM1: In-Line Probing Analysis of Riboswitches
Elizabeth E. Regulski and Ronald R. Breaker

ESM2: Analysis of the RNA Backbone: Structural Analysis of Riboswitches by In-Line Probing and Selective 2'-Hydroxyl Acylation and Primer Extension (SHAPE)
Catherine A. Wakeman1 and Wade C. Winkler