Journal
BMC GENOMICS
Volume 11, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1471-2164-11-414
Keywords
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Funding
- Helse Sor-Ost/University of Oslo Microarray Core Facility
- Research Council of Norway
- Norwegian Research Council
- German Research Foundation [WA 2713/1-1]
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Background: The method of chromatin immunoprecipitation combined with microarrays (ChIP-Chip) is a powerful tool for genome-wide analysis of protein binding. However, a high background signal is a common phenomenon. Results: Reinvestigation of the chromatin immunoprecipitation procedure led us to discover four causes of high background: i) non-unique sequences, ii) incomplete reversion of crosslinks, iii) retention of protein in spin-columns and iv) insufficient RNase treatment. The chromatin immunoprecipitation method was modified and applied to analyze genome-wide binding of SeqA and sigma(32) in Escherichia coli. Conclusions: False positive findings originating from these shortcomings of the method could explain surprising and contradictory findings in published ChIP-Chip studies. We present a modified chromatin immunoprecipitation method greatly reducing the background signal.
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