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antibodies-online CUT&RUN and CUT&Tag Handbook

Written/Edited by Julian Pampel BSc
antibodies-online cutrun-cuttag Handbookantibodies-online CUT&RUN and CUT&Tag Handbook Handbook

Download our CUT&RUN and CUT&Tag Handbook!

In early 2017 a publication from Steven Henikoff’s lab at the Fred Hutchinson Cancer Research Center described CUT&RUN. CUT&RUN combines elements of ChIP-seq and ChIC but is superior to both methods because of its exceptionally low sample input and superior signal-to-noise ratio. The method has since found wide adoption in the epigenetics field and increasingly also beyond.

antibodies-online has compiled a handbook describing the intricacies of CUT&RUN (relying on targeted MNase DNA fragmentation) and the related method CUT&Tag (using directed tagmentation instead). This handbook gives a short overview of CUT&RUN and CUT&Tag. Subsequently, detailed step-by-step protocols are provided based on Skene PJ and Henikoff S (2017) Nature Protocols and Meers MP et al. (2019) eLIFE for CUT&RUN and Kaya-Okur HS et al. (2019) Nature Communications and Kaya-Okur HS et Kaya-Okur HS et al. (2020) Nature Protocols for CUT&Tag.

Version 1.4 features:

  • Advantages of CUT&RUN and CUT&Tag in comparison with other epigenetic techniques, eg. ChIP-seq
  • Step-by-step protocol*Update*
  • Major FAQ on practical application questions*Update*
  • All reagents required in one list

SARS-CoV-2 Handbook: Table of Contents


  • Advantages of CUT&RUN
  • Direct or indirect CUT&RUN
  • Chromatin cleavage at high Ca2+/low salt concentration
  • Accurate quantitation with heterologous spike-in DNA or carry-over E.coli DNA
  • CUT&RUN Reagents
  • Reagent Preparation
  • Protocol
  • Overview CUT&Tag

2. CUT&Tag:

  • Advantages of CUT&Tag
  • Reagents Required
  • CUT&Tag Reagents
  • Protocol
  • Overview CUT&Tag

3. Supplementary Material:

  • Recommended Antibodies for CUT&RUN and CUT&Tag
  • Frequently Asked Questions
  • References

More Resources for CUT&RUN and CUT&Tag

CUT&RUN Introduction Webinar

CUT&Tag: Workflow and Epigenetic Antibodies

Julian Pampel
Julian Pampel BSc
Content Manager at

Creative mind of antibodies-online with a keen eye for details. Proficient in the field of life-science with a passion for plant biotechnology and clinical study design. Responsible for illustrated and written content at antibodies-online as well as supervision of the antibodies-online scholarship program.

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