ChIP on Chip: surprising results are often artifacts
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results<...
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| Format: | Article |
| Language: | English |
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BMC
2010-07-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/414 |
| _version_ | 1818230400764346368 |
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| author | Skarstad Kirsten Waldminghaus Torsten |
| author_facet | Skarstad Kirsten Waldminghaus Torsten |
| author_sort | Skarstad Kirsten |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 σ<sup>32 </sup>in <it>Escherichia coli</it>.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-12T10:33:54Z |
| format | Article |
| id | doaj.art-bef4500c8cfc4b6c92c32e0cd5ca3bca |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T10:33:54Z |
| publishDate | 2010-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-bef4500c8cfc4b6c92c32e0cd5ca3bca2022-12-22T00:27:16ZengBMCBMC Genomics1471-21642010-07-0111141410.1186/1471-2164-11-414ChIP on Chip: surprising results are often artifactsSkarstad KirstenWaldminghaus Torsten<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 σ<sup>32 </sup>in <it>Escherichia coli</it>.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/11/414 |
| spellingShingle | Skarstad Kirsten Waldminghaus Torsten ChIP on Chip: surprising results are often artifacts BMC Genomics |
| title | ChIP on Chip: surprising results are often artifacts |
| title_full | ChIP on Chip: surprising results are often artifacts |
| title_fullStr | ChIP on Chip: surprising results are often artifacts |
| title_full_unstemmed | ChIP on Chip: surprising results are often artifacts |
| title_short | ChIP on Chip: surprising results are often artifacts |
| title_sort | chip on chip surprising results are often artifacts |
| url | http://www.biomedcentral.com/1471-2164/11/414 |
| work_keys_str_mv | AT skarstadkirsten chiponchipsurprisingresultsareoftenartifacts AT waldminghaustorsten chiponchipsurprisingresultsareoftenartifacts |