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  Standardizing chromatin research: a simple and universal emthod for ChIP-seq

Arrigoni, L., Richter, A. S., Betancourt, E., Bruder, K., Diehl, S., Manke, T., et al. (2016). Standardizing chromatin research: a simple and universal emthod for ChIP-seq. Nucleic Acids Research (London), 44, e67. doi:doi: 10.1093/nar/gkv1495.

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 Creators:
Arrigoni, Laura1, Author
Richter, Andreas S.2, Author              
Betancourt, Emily1, Author
Bruder, Kerstin1, Author
Diehl, Sarah3, Author
Manke, Thomas2, Author              
Bönisch, Ulrike1, Author
Affiliations:
1Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, 79108 Freiburg, DE, ou_2243640              
2Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243644              
3Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Belvaux, Luxembourg, ou_persistent22              

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 Abstract: Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a key technique in chromatin research. Although heavily applied, existing ChIP-seq protocols are often highly fine-tuned workflows, optimized for specific experimental requirements. Especially the initial steps of ChIP-seq, particularly chromatin shearing, are deemed to be exceedingly cell-type-specific, thus impeding any protocol standardization efforts. Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (NEXSON: Nuclei EXtraction by SONication) that is highly effective across various organisms, cell types and cell numbers. The described method has the potential to replace complex cell-type-specific, but largely ineffective, nuclei isolation protocols. By including NEXSON in ChIP-seq workflows, we completely eliminate the need for extensive optimization and sample-dependent adjustments. Apart from this significant simplification, our approach also provides the basis for a fully standardized ChIP-seq and yields highly reproducible transcription factor and histone modifications maps for a wide range of different cell types. Even small cell numbers (∼10 000 cells per ChIP) can be easily processed without application of modified chromatin or library preparation protocols.

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Language(s): eng - English
 Dates: 2016-04-20
 Publication Status: Published in print
 Pages: 13
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: doi: 10.1093/nar/gkv1495
 Degree: -

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Title: Nucleic Acids Research (London)
  Other : Nucleic Acids Res
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: 13 Volume / Issue: 44 Sequence Number: - Start / End Page: e67 Identifier: Other: 110992357379342
ISSN: 0305-1048
CoNE: https://pure.mpg.de/cone/journals/resource/110992357379342