Title |
ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
|
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Published in |
BMC Genomics, February 2011
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DOI | 10.1186/1471-2164-12-134 |
Pubmed ID | |
Authors |
Joshua WK Ho, Eric Bishop, Peter V Karchenko, Nicolas Nègre, Kevin P White, Peter J Park |
Abstract |
Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. |
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Unknown | 2 | 50% |
Demographic breakdown
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Members of the public | 1 | 25% |
Mendeley readers
Geographical breakdown
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Researcher | 117 | 24% |
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Other | 20 | 4% |
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Engineering | 8 | 2% |
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