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ChIP-Seq: technical considerations for obtaining high-quality data

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Abstract

Chromatin immunoprecipitation followed by next-generation sequencing analysis (ChIP-Seq) is a powerful method with which to investigate the genome-wide distribution of chromatin-binding proteins and histone modifications in any genome with a known sequence. The application of this technique to a variety of developmental and differentiation systems has provided global views of the cis-regulatory elements, transcription factor function and epigenetic processes involved in the control of gene transcription. Here we describe several technical aspects of the ChIP-Seq assay that diminish bias and background noise and allow the consistent generation of high-quality data.

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Figure 1: ChIP-Seq experimental design.
Figure 2: Common procedures for ChIP-seq data analysis.

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Acknowledgements

We thank B. Abraham and D. Northrup for critical reading of the manuscript, and K. Cui for discussions. Supported by the Division of Intramural Research of the National Heart, Lung and Blood Institute.

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Authors and Affiliations

  1. Benjamin L. Kidder, Gangqing Hu and Keji Zhao are in the Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.,

    Benjamin L Kidder, Gangqing Hu & Keji Zhao

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  1. Benjamin L Kidder
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  2. Gangqing Hu
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  3. Keji Zhao
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Correspondence to Benjamin L Kidder or Keji Zhao.

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Kidder, B., Hu, G. & Zhao, K. ChIP-Seq: technical considerations for obtaining high-quality data. Nat Immunol 12, 918–922 (2011). https://doi.org/10.1038/ni.2117

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