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RNA

Methods and Protocols

  • Book
  • © 2011

Overview

Editors:
  1. Henrik Nielsen

    1. The Panum Institute, Dept. of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark

    View editor publications

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  • 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
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 703)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xv
    Download chapter PDF

  2. RNA Methods

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. The Transcriptional Landscape

      • Henrik Nielsen
      Pages 3-14

    3. Working with RNA

      • Henrik Nielsen
      Pages 15-28

    4. Synthesis of RNA by In Vitro Transcription

      • Bertrand Beckert, Benoît Masquida
      Pages 29-41

    5. Efficient Poly(A)+ RNA Selection Using LNA Oligo(T) Capture

      • Nana Jacobsen, Jens Eriksen, Peter Stein Nielsen
      Pages 43-51

    6. Genome Browsers

      • Elfar Torarinsson
      Pages 53-65

    7. Web-Based Tools for Studying RNA Structure and Function

      • Ajish D. George, Scott A. Tenenbaum
      Pages 67-86

    8. Northern Blotting Analysis

      • Knud Josefsen, Henrik Nielsen
      Pages 87-105

    9. Rapid Amplification of cDNA Ends (RACE)

      • Oladapo Yeku, Michael A. Frohman
      Pages 107-122

    10. Fractionation of mRNA Based on the Length of the Poly(A) Tail

      • Hedda A. Meijer, Cornelia H. de Moor
      Pages 123-135

    11. Analysis of Mutations that Influence Pre-mRNA Splicing

      • Zhaiyi Zhang, Stefan Stamm
      Pages 137-160

    12. S1 Nuclease Analysis of Alternatively Spliced mRNA

      • Martin Lützelberger, Jørgen Kjems
      Pages 161-171

    13. Promises and Challenges in Developing RNAi as a Research Tool and Therapy

      • Mouldy Sioud
      Pages 173-187

    14. Inhibition of Gene Function in Mammalian Cells Using Short-Hairpin RNA (shRNA)

      • Jørn Remi Henriksen, Jochen Buechner, Cecilie Løkke, Trond Flægstad, Christer Einvik
      Pages 189-204

    15. Validation of RNAi by Real Time PCR

      • Knud Josefsen, Ying C. Lee
      Pages 205-217

    16. Profiling RNA Polymerase II Using the Fast Chromatin Immunoprecipitation Method

      • Joel Nelson, Oleg Denisenko, Karol Bomsztyk
      Pages 219-234

  3. RNP Methods

    1. Front Matter

      Pages 235-235
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    2. The Post-transcriptional Operon

      • Scott A. Tenenbaum, Jan Christiansen, Henrik Nielsen
      Pages 237-245

    3. 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 et al.
      Pages 247-263
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Keywords

About this book

Recent insight into the transcripts generated from the mammalian genome (i.e. the transcriptome) has revealed that transcription is a far more complex phenomenon than previously thought. In RNA: Methods and Protocols, expert researchers provide the procedures and methods used to describe the structure of messenger RNAs and non-coding RNAs that are transcribed by RNA polymerase II as the immediate gene products in mammalian cells. Focused on the structure of the RNA products of “gene X” and the mapping of proteins associated with these RNAs, the volume presents appropriate information for non-specialists in RNA biology. Written in the highly successful Methods in Molecular Biology™ series format, many chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, RNA: Methods and Protocols views the transcriptional landscape with an appreciation for the role that proteins play in the processing and interpretation of genetic information in an attempt to further our crucial knowledge of the many products and sophisticated regulatory networks that result from it.

Editors and Affiliations

  • The Panum Institute, Dept. of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark

    Henrik Nielsen

Bibliographic Information

  • Book Title: RNA

  • Book Subtitle: Methods and Protocols

  • Editors: Henrik Nielsen

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-248-9

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2011

  • Hardcover ISBN: 978-1-58829-913-0Published: 10 December 2010

  • Softcover ISBN: 978-1-4939-5643-2Published: 30 April 2017

  • eBook ISBN: 978-1-59745-248-9Published: 02 December 2010

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XV, 329

  • Topics: Human Genetics, Gene Expression

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