Small Non-Coding RNAs, 2015 Methods and Protocols Methods in Molecular Biology Series, Vol. 1296

This volume contains state-of-the-art methods tackling all aspects of small non-coding RNAs biology.  Small Non-Coding RNAs: Methods and Protocols guides readers through customized dedicated protocols and technologies that will be of valuable help to all those willing to contribute deciphering the numerous functions of small non-coding RNAs. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and key tips on troubles troubleshooting and avoiding known pitfalls.

Instructive and practical, Small Non-Coding RNAs: Methods and Protocols reaches out to biochemists, cellular and molecular biologists already working in the field of RNA biology  and to those just starting to study small non-coding RNAs.

Part I Introduction to Small Non-Coding RNAs

1. Small Non-Coding RNAs: A Quick Look in the Rear-View Mirror
Guillaume Clerget, Yoann Abel, and Mathieu Rederstorff

2.Alcoholic Precipitation of Small Non-Coding RNAs
Guillaume Clerget, Valérie Bourguignon-Igel, and Mathieu Rederstorff

3.Quantification and Quality Control of a Small Non-Coding RNA Preparation
Virginie Marchand and Christiane Branlant

4. Impact of RNA Isolation Protocols on RNA Detection by Northern Blotting
Katrin Damm, Simone Bach, Katrin M. H. Müller, Gabriele Klug, Olga Y. Burenina,Elena A. Kubareva, Arnold Grünweller, and Roland K. Hartmann

Part II Visualization and Analysis of Small Non-Coding RNAs

5. Improved Northern Blot Detection of Small RNAs Using EDC Crosslinking and DNA/LNA Probes
Katrin Damm, Simone Bach, Katrin M. H. Müller, Gabriele Klug, Olga Y. Burenina,Elena A. Kubareva, Arnold Grünweller, and Roland K. Hartmann

6. Direct Cloning of Double Stranded RNAs
Manli Shen, Marina Falaleeva, Natalia Korotkova, and Stefan Stamm

7. Detection and Labeling of Small Non-Coding RNAs by Splinted Ligation
Gabrielle Bourgeois, Florian Chardon, Anne-Sophie Tillault, and Magali Blaud

8. Fluorescence in situ Hybridization of Small Non-Coding RNAs
Valentin Vautrot, Christelle Aigueperse, Christiane Branlant, and Isabelle Behm-Ansmant

9. RT-qPCR Based Quantification of Small Non-Coding RNAs
Fjoralba Zeka, Pieter Mestdagh, and Jo Vandesompele

10.Stem-Loop RT-PCR Based Quantification of Small Non-Coding RNAsVéronique Salone and Mathieu Rederstorff

11. miR-RACE: An Effective Approach to Accurately Determine the Sequence of Computationally Identified miRNAs
Chen Wang and Jinggui Fang

12. Probing Small Non-Coding RNAs StructuresJean-Vincent Philippe, Lilia Ayadi, Christiane Branlant, and Isabelle Behm-Ansmant

Part III High-Throughput Approaches to Study Non-Coding RNAs 

13.cDNA Library Generation for the Analysis of Small RNAs by High Throughput Sequencing
Jennifer Gebetsberger, Roger Fricker, and Norbert Polacek

14. CLIP-seq to Discover Transcriptome-Wide Imprinting of RNA Binding Proteins in Living Cells
Jérôme Saulière and Hervé Le Hir

15. Microarray Analysis of Small Non-Coding RNAs
Michael Karbiener and Marcel Scheideler

Part IV Small Non-Coding RNAs Applications

16. RLM-RACE, PPM-RACE and qRT-PCR, an Integrated Strategy to Accurately Validate miRNA Target Genes
Chen Wang and Jinggui Fang

17. Dual Luciferase Gene Reporter Assays to Study miRNA Function
Thomas Clément, Véronique Salone, and Mathieu Rederstorff

18. Gene Expression Knockdown by Transfection of siRNAs into Mammalian Cells
Yoann Abel and Mathieu Rederstorff

19. Efficient and Selective Knockdown of Small Non-Coding RNAs
Xue-Hai Liang, Wen Shen, and Stanley T. Crooke

20. Cell-SELEX: In Vitro Selection of Synthetic Small Specific Ligands
Helena Dickinson, Melanie Lukasser, Günter Mayer, and Alexander Hüttenhofer

21. Small Non-Coding RNAs and Aptamers in Diagnostics and Therapeutics
Marissa Leonard, Yijuan Zhang, and Xiaoting Zhang

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts