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Successful implementation of ChIP-seq antibody quality control at Diagenode using automated ChIP protocol on the SX-8G IP-Star® Compact

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Chromatin immunoprecipitation (ChIP) is the most widely used method to study protein-DNA interactions. A successful ChIP, however, is largely depending on the use of well characterized, highly specific ChIP-grade antibodies.

ChIP-seq has become the gold standard for whole-genome mapping of protein-DNA interactions. The generalized adoption of this technology is currently limited by four main technical hurdles. First, the reproducibility and biological relevance of DNA-associated protein landscapes depend on the specificity and performance of the antibodies in the context for which they are used. Second, the ChIP-seq method requires optimized protocols ensuring high recovery and increased signal-to-noise ratio. Third, as an effort to reduce the cost per sample and improve reproducibility, the ChIP-seq method should be compatible with automation. Finally, the economical and widespread use of ChIP-seq requires access to a fast and high value/quality next-generation sequencing platform. Here, we demonstrate the successful use of the Diagenode integrated line of products to establish a QC procedure to qualify antibodies and standardize ChIP-seq experiments.

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Correspondence to Ignacio Mazon.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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  • Chromatin Immunoprecipitation
  • High Recovery
  • Biological Relevance
  • Sequencing Platform
  • Technical Hurdle