Main description:

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.

Contents:

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

Neus Visa and Antonio Jordan-Pla

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

Antonio Jordan-Pla and Neus Visa

3. How to Combine ChIP with qPCR

Patrik Asp

4. Analysis of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Tiling Microarray (ChIP-on-Chip)

Hui Gao and Chunyan Zhao

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

Mario A.F. Soares and Diogo S. Castro

6. Chromatin RNA Immunoprecipitation (ChRIP)

Tanmoy Mondal, Santhilal Subhash, and Chandrasekhar Kanduri

7. DNA Accessibility by MNase Digestions

Ann-Kristin OEstlund Farrants

8. Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-Seq)

Wieteke Anna Maria Hoeijmakers and Richard Bartfai

9. ChIP-re-ChIP: Co-Occupancy Analysis by Sequential Chromatin Immunoprecipitation

Timothy V. Beischlag, Gratien G. Prefontaine, and Oliver Hankinson

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

Roubina Tatavosian, and Xiaojun Ren

11. Chromatin Immunoprecipitation of Skeletal Muscle Tissue

Amarjit Saini and Carl Johan Sundberg

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

Kun Wang and Ann-Christin Lindas

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

Brett R. Hanson and Ming Tan

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

Teodora Ribarska and Gregor D. Gilfillan

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

Shenqi Wang and On Sun Lau

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

Christophe D. Chabbert, Sophie H. Adjalley, Lars M. Steinmetz, and Vicente Pelechano

17. Analysis of ChIP-Seq Data in R/Bioconductor

Ines de Santiago and Thomas Carroll

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

Andrea B. Eberle