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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.

The version of September 2022 features:

  • The CUT&RUN Low Volume Urea protocol which enables in situ profiling of rare transcription factors and non-direct DNA binding cofactors
  • A wide range of antibodies validated for CUT&RUN
  • Major FAQ on practical application questions*Update*
  • More background information on the development of epigenetic techniques alongside with a chronological visualization

SARS-CoV-2 Handbook: Table of Contents

1. Introduction:

  • Background
  • Timeline of selected epigenetics techniques


  • About the method
  • 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
  • Protocol: Low Salt
  • Reagents Required and Preparation
  • Overview CUT&RUN workflow
  • Step-by-step protocol
  • Protocol: Low Volume Urea
  • Reagents Required and Preparation
  • Overview CUT&RUN workflow
  • Step-by-step protocol

3. CUT&Tag:

  • Advantages of CUT&Tag
  • Protocol:
  • Reagents Required and Preparation
  • Overview CUT&RUN workflow
  • Step-by-step protocol

4. 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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