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Nucleic Acids Research Advance Access published online on January 18, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn001
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events

Steve Flanagin1, Joel D. Nelson2, David G. Castner3, Oleg Denisenko1 and Karol Bomsztyk1,2,*

1UW Medicine Lake Union, Department of Medicine, University of Washington, Seattle, WA 98109, 2Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98109, 3National ESCA and Surface Analysis Center for Biomedical Problems, Departments of Bioengineering and Chemical Engineering, University of Washington, Seattle, WA 98195, USA

*To whom correspondence should be addressed. Tel: +1 206 616 7949; Fax: +1 206 616 8591; Email: karolb{at}u.washington.edu

Received December 12, 2007. Revised December 28, 2007. Accepted December 31, 2007.

The chromatin immunoprecipitation (ChIP) assay is a major tool in the study of genomic processes in vivo. This and other methods are revealing that control of gene expression, cell division and DNA repair involves multiple proteins and great number of their modifications. ChIP assay is traditionally done in test tubes limiting the ability to study signaling of the complex genomic events. To increase the throughput and to simplify the assay we have developed a microplate-based ChIP (Matrix ChIP) method, where all steps from immunoprecipitation to DNA purification are done in microplate wells without sample transfers. This platform has several important advantages over the tube-based assay including very simple sample handling, high throughput, improved sensitivity and reproducibility, and potential for automation. 96 ChIP measurements including PCR can be done by one researcher in one day. We illustrate the power of Matrix ChIP by parallel profiling 80 different chromatin and transcription time-course events along an inducible gene including transient recruitment of kinases.


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