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RNA Mapping

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. M. Lucrecia Alvarez

    1. Diabetes, Cardiovascular, and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, USA

  2. Mahtab Nourbakhsh

    1. Department of Plastic Surgery, University Hospital of the RWTH Aachen, Germany

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1182)

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About this book

In RNA Mapping- Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used to study RNA. These include protocols for the consequence of the emerging interest in the characterization of cellular RNAs urged by their potential use as diagnostic biomarkers or therapeutic targets. In particular, the biological relevance of microRNAs in human physiology and disease development is highlighted in the 16 chapters focused on methods for their physical and functional mapping. Written in the highly successful Methods in 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 troubleshooting and avoiding known pitfalls.

Authoritative and practical, RNA Mapping- Methods and Protocols provides instruction and inspiration for scientists who are facing the challenges of the discovery and/or functional characterization of RNA molecules for a wide variety of applications ranging from novel biomedical diagnostics to therapeutics and biomaterials.

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Table of contents (28 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Structural RNA Mapping

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Full-Length Characterization of Transcribed Genomic Regions

      • Marc R. Reboll, M. Lucrecia Alvarez, Mahtab Nourbakhsh
      Pages 3-18

    3. Rapid Mapping of RNA 3′ and 5′ Ends

      • Victoria Zismann, Mahtab Nourbakhsh
      Pages 19-25

    4. Single Nucleotide Mapping of RNA 5′ and 3′ Ends

      • Mahtab Nourbakhsh
      Pages 27-34

    5. Analysis of RNA Secondary Structure

      • Mahtab Nourbakhsh
      Pages 35-42

    6. Tertiary Structure Mapping of the Pri-miRNA miR-17~92

      • Steven G. Chaulk, Richard P. Fahlman
      Pages 43-55

    7. In Situ Hybridization Detection of miRNA Using LNA™ Oligonucleotides

      • Stefania Cotta Doné, Olga Beltcheva
      Pages 57-71

    8. Quantification of miRNAs by a Simple and Specific qPCR Method

      • Susanna Cirera, Peter K. Busk
      Pages 73-81

    9. RNA Isolation for Small RNA Next-Generation Sequencing from Acellular Biofluids

      • Kasandra L. Burgos, Kendall Van Keuren-Jensen
      Pages 83-92

    10. Sequencing Small RNA: Introduction and Data Analysis Fundamentals

      • Jai Prakash Mehta
      Pages 93-103

    11. Measuring Expression Levels of Small Regulatory RNA Molecules from Body Fluids and Formalin-Fixed, Paraffin-Embedded Samples

      • Adrienn Gyongyosi, Otto Docs, Zsolt Czimmerer, Laszlo Orosz, Attila Horvath, Olga Török et al.
      Pages 105-119

    12. MicroRNA Profiling in Plasma or Serum Using Quantitative RT-PCR

      • Marina C. Costa, Ana Lúcia Leitão, Francisco J. Enguita
      Pages 121-129

    13. MicroRNA Profiling of Exosomes Isolated from Biofluids and Conditioned Media

      • Sweta Rani
      Pages 131-144

    14. Isolation of Urinary Exosomes for RNA Biomarker Discovery Using a Simple, Fast, and Highly Scalable Method

      • M. Lucrecia Alvarez
      Pages 145-170

  3. Functional RNA Mapping

    1. Front Matter

      Pages 171-171
      Download chapter PDF

    2. Identification of Actively Translated mRNAs

      • Marc R. Reboll, Mahtab Nourbakhsh
      Pages 173-178

    3. Mapping of Internal Ribosome Entry Sites (IRES)

      • Sarah Mehrtens, Marc R. Reboll
      Pages 179-185

    4. Mapping of Protein Binding RNA Elements

      • Marc R. Reboll
      Pages 187-194

    5. Purification of RNA-Binding Proteins

      • Birgit Ritter, Marc R. Reboll
      Pages 195-201
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Editors and Affiliations

  • Diabetes, Cardiovascular, and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, USA

    M. Lucrecia Alvarez

  • Department of Plastic Surgery, University Hospital of the RWTH Aachen, Germany

    Mahtab Nourbakhsh

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Bibliographic Information

  • Book Title: RNA Mapping

  • Book Subtitle: Methods and Protocols

  • Editors: M. Lucrecia Alvarez, Mahtab Nourbakhsh

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-1062-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2014

  • Hardcover ISBN: 978-1-4939-1061-8Published: 24 July 2014

  • Softcover ISBN: 978-1-4939-5386-8Published: 17 September 2016

  • eBook ISBN: 978-1-4939-1062-5Published: 23 July 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 375

  • Number of Illustrations: 20 b/w illustrations, 53 illustrations in colour

  • Topics: Human Genetics, Gene Function

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