ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

  • Ho J
  • Bishop E
  • Karchenko P
 et al. 
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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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Authors

  • Nicolas NegreUniversite Montpellier Faculte des Sciences de Montpellier

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  • Joshua W.K. Ho

  • Eric Bishop

  • Peter V. Karchenko

  • Kevin P. White

  • Peter J. Park

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