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Long Non-Coding RNAs

Methods and Protocols

  • Book
  • © 2016

Overview

Editors:
  1. Yi Feng

    1. School of Medicine, University of Pennsylvania, Philadelphia, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Lin Zhang

    1. School of Medicine, University of Pennsylvania, Philadelphia, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1402)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. LncRNA Pulldown Combined with Mass Spectrometry to Identify the Novel LncRNA-Associated Proteins

    • Zhen Xing, Chunru Lin, Liuqing Yang
    Pages 1-9

  3. Cross-Linking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions Between Long Noncoding RNAs and RNA-Binding Proteins

    • Je-Hyun Yoon, Myriam Gorospe
    Pages 11-17

  4. Characterization of Long Noncoding RNA-Associated Proteins by RNA-Immunoprecipitation

    • Youyou Zhang, Yi Feng, Zhongyi Hu, Xiaowen Hu, Chao-Xing Yuan, Yi Fan et al.
    Pages 19-26

  5. Isolation of Protein Complexes Associated with Long Noncoding RNAs

    • Kiranmai Gumireddy, Jinchun Yan, Qihong Huang
    Pages 27-32

  6. Profiling Long Noncoding RNA Expression Using Custom-Designed Microarray

    • Xinna Zhang, Gabriel Lopez-Berestein, Anil K. Sood, George A. Calin
    Pages 33-41

  7. Long Noncoding RNA Expression Profiling Using Arraystar LncRNA Microarrays

    • Yanggu Shi, Jindong Shang
    Pages 43-61

  8. Nuclear RNA Isolation and Sequencing

    • Navroop K. Dhaliwal, Jennifer A. Mitchell
    Pages 63-71

  9. Targeted LncRNA Sequencing with the SeqCap RNA Enrichment System

    • John C. Tan, Venera D. Bouriakov, Liang Feng, Todd A. Richmond, Daniel Burgess
    Pages 73-100

  10. ChIP-Seq: Library Preparation and Sequencing

    • Karyn L. Sheaffer, Jonathan Schug
    Pages 101-117

  11. Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

    • Arturo V. Orjalo Jr., Hans E. Johansson
    Pages 119-134

  12. Simultaneous RNA–DNA FISH

    • Lan-Tian Lai, Zhenyu Meng, Fangwei Shao, Li-Feng Zhang
    Pages 135-145

  13. Visualizing Long Noncoding RNAs on Chromatin

    • Michael Hinten, Emily Maclary, Srimonta Gayen, Clair Harris, Sundeep Kalantry
    Pages 147-164

  14. Non-isotopic Method for In Situ LncRNA Visualization and Quantitation

    • Botoul Maqsodi, Corina Nikoloff
    Pages 165-176

  15. Detection of Long Noncoding RNA Expression by Nonradioactive Northern Blots

    • Xiaowen Hu, Yi Feng, Zhongyi Hu, Youyou Zhang, Chao-Xing Yuan, Xiaowei Xu et al.
    Pages 177-188

  16. Assessment of In Vivo siRNA Delivery in Cancer Mouse Models

    • Hiroto Hatakeyama, Sherry Y. Wu, Lingegowda S. Mangala, Gabriel Lopez-Berestein, Anil K. Sood
    Pages 189-197

  17. Targeting Long Noncoding RNA with Antisense Oligonucleotide Technology as Cancer Therapeutics

    • Tianyuan Zhou, Youngsoo Kim, A. Robert MacLeod
    Pages 199-213

  18. Characterization of Circular RNAs

    • Yang Zhang, Li Yang, Ling-Ling Chen
    Pages 215-227

  19. Methods for Characterization of Alternative RNA Splicing

    • Samuel E. Harvey, Chonghui Cheng
    Pages 229-241

  20. NONCODEv4: Annotation of Noncoding RNAs with Emphasis on Long Noncoding RNAs

    • Yi Zhao, Jiao Yuan, Runsheng Chen
    Pages 243-254
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Keywords

About this book

This volume assembles a broad spectrum of methods used in long non-coding RNAs (lncRNA) research, ranging from computational annotation of lncRNA genes to molecular and cellular analyses of the function of individual lncRNA. Long Non-Coding RNAs: Methods and Protocols also discusses methods used to study circular RNAs and RNA splicing, as well as influential findings on lncRNA in human diseases. 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 tips on troubleshooting and avoiding known pitfalls.
Thorough and cutting-edge, Long Non-Coding RNAs: Methods and Protocols is a must-have for molecular biologists, cell and developmental biologists, specialists who conduct disease-oriented research, and bioinformatics experts who seek a better understanding on lncRNA expression and function by computational analysis of the massive sequencing data that are rapidly accumulating in recent years.

Editors and Affiliations

  • School of Medicine, University of Pennsylvania, Philadelphia, USA

    Yi Feng, Lin Zhang

Bibliographic Information

  • Book Title: Long Non-Coding RNAs

  • Book Subtitle: Methods and Protocols

  • Editors: Yi Feng, Lin Zhang

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3378-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3376-1Published: 01 January 2016

  • Softcover ISBN: 978-1-4939-8035-2Published: 31 March 2018

  • eBook ISBN: 978-1-4939-3378-5Published: 31 December 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 298

  • Number of Illustrations: 13 b/w illustrations, 40 illustrations in colour

  • Topics: Human Genetics

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