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Chromatin Immunoprecipitation

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Neus Visa

    1. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden

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    You can also search for this editor in PubMed   Google Scholar

  2. Antonio Jordán-Pla

    1. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques for the study of chromatin immunoprecipitation
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1689)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. ChIP and ChIP-Related Techniques: Expanding the Fields of Application and Improving ChIP Performance

    • Neus Visa, Antonio Jordán-Pla
    Pages 1-7

  3. Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments

    • Antonio Jordán-Pla, Neus Visa
    Pages 9-28

  4. How to Combine ChIP with qPCR

    • Patrik Asp
    Pages 29-42

  5. Analysis of Protein–DNA Interaction by Chromatin Immunoprecipitation and DNA Tiling Microarray (ChIP-on-chip)

    • Hui Gao, Chunyan Zhao
    Pages 43-51

  6. Chromatin Immunoprecipitation from Mouse Embryonic Tissue or Adherent Cells in Culture, Followed by Next-Generation Sequencing

    • Mário A. F. Soares, Diogo S. Castro
    Pages 53-63

  7. Chromatin RNA Immunoprecipitation (ChRIP)

    • Tanmoy Mondal, Santhilal Subhash, Chandrasekhar Kanduri
    Pages 65-76

  8. DNA Accessibility by MNase Digestions

    • Ann-Kristin Östlund Farrants
    Pages 77-82

  9. Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq)

    • Wieteke Anna Maria Hoeijmakers, Richárd Bártfai
    Pages 83-101

  10. ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation

    • Timothy V. Beischlag, Gratien G. Prefontaine, Oliver Hankinson
    Pages 103-112

  11. Sm-ChIPi: Single-Molecule Chromatin Immunoprecipitation Imaging

    • Roubina Tatavosian, Xiaojun Ren
    Pages 113-126

  12. Chromatin Immunoprecipitation of Skeletal Muscle Tissue

    • Amarjit Saini, Carl Johan Sundberg
    Pages 127-138

  13. Chromatin Immunoprecipitation Assay in the Hyperthermoacidophilic Crenarchaeon, Sulfolobus acidocaldarius

    • Kun Wang, Ann-Christin Lindås
    Pages 139-146

  14. Using Intra-ChIP to Measure Protein–DNA Interactions in Intracellular Pathogens

    • Brett R. Hanson, Ming Tan
    Pages 147-155

  15. Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers

    • Teodora Ribarska, Gregor D. Gilfillan
    Pages 157-166

  16. MOBE-ChIP: Probing Cell Type-Specific Binding Through Large-Scale Chromatin Immunoprecipitation

    • Shenqi Wang, On Sun Lau
    Pages 167-176

  17. Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis

    • Christophe D. Chabbert, Sophie H. Adjalley, Lars M. Steinmetz, Vicent Pelechano
    Pages 177-194

  18. Analysis of ChIP-seq Data in R/Bioconductor

    • Ines de Santiago, Thomas Carroll
    Pages 195-226

  19. Spike-In Normalization of ChIP Data Using DNA–DIG–Antibody Complex

    • Andrea B. Eberle
    Pages 227-238

  20. Back Matter

    Pages 239-243
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Keywords

About this book

This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP-related methods in a variety of biological research areas. The collection also includes protocols designed to improve the performance of ChIP for specific applications.  Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols features techniques, including bioinformatic analysis of ChIP data, will be of interest to a very broad research community in the fields of biochemistry, molecular biology, microbiology, and biomedicine.

Editors and Affiliations

  • Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden

    Neus Visa, Antonio Jordán-Pla

Bibliographic Information

  • Book Title: Chromatin Immunoprecipitation

  • Book Subtitle: Methods and Protocols

  • Editors: Neus Visa, Antonio Jordán-Pla

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7380-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7379-8Published: 14 October 2017

  • Softcover ISBN: 978-1-4939-8467-1Published: 14 August 2018

  • eBook ISBN: 978-1-4939-7380-4Published: 12 October 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 243

  • Number of Illustrations: 9 b/w illustrations, 26 illustrations in colour

  • Topics: Biochemistry, general

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