Chromatin Immunoprecipitation: Methods and Protocols

ISBN-13: 9781493984671 / Angielski / Miękka / 2018 / 243 str.

Neus Visa; Antonio Jordan-Pla

Spis treści

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

            Neus Visa and Antonio Jordán-Pla

 

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

            Antonio Jordán-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

            Mário 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 Östlund Farrants

 

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

            Wieteke Anna Maria Hoeijmakers and Richárd Bártfai

 

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 Lindås

 

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

Blurb

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.