CUT&RUN Handbook:

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CUT&RUN: Better than ChIP-seq!

Data taken from: J. Skene & Steven Henikoff (2018), Nature Volume 13  

New CUT&RUN Sets for mapping Protein-DNA Interaction

CUT&RUN Pro Complete ABIN6923135
CUT&RUN Pro Direct ABIN6923136
CUT&RUN Pro Sec ABIN6923137
CUT&RUN Core Complete ABIN6923131
CUT&RUN Core Direct ABIN6923132
CUT&RUN Core Sec ABIN6923133

Better Data

Only 1/3 of sequencing Reads required

Less Noise

Easier Peak-Calling Higher Reproducibility

Less Sample

10 x less Sample in comparison to ChIP-seq 

Obtain purified DNA from Cells within 1 Day


CUT&RUN: Workflow

Proven Components

First set of matching high quality reagents on the market gives you a worry free access to CUT&RUN. 


A single source ensures a consistent set of reagents and protocol. Long-term availability and reproducibility guaranteed. 

Save Time and Money

Get the CUT&RUN set tailored to your needs and save money compared to purchasing the components separately. 



Our Sets include the following Components:

CUT&RUN is performed on intact cells or nuclei without fragmentation. The cleaved chromatin complexes diffuse out of the nuclei where they can be harvested in supernatant. 

An antibody against the protein or histone modification of interest is bound to chromatin in situ. Subsequently, a Protein A-micrococcal nuclease (pA-MNase) or Protein A and Protein G micrococcal nuclease (pAG-MNase) fusion protein is tethered to the Fc region of the antibody. The nuclease then cleaves around the target. 

Antigen recognition can either be direct or indirect via a secondary antibody (see figure below). 

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CUT&RUN offers a new approach to study Protein-DNA interaction. CUT&RUN overcomes various downfalls of ChIP-Seq with improved workflow. Especially the background noise is significantly reduced.

Cleavage Under Targets & Release Using Nuclease 





Positive and Negative Control Antibodies are important to assess cleavage and chromatin release without the need to sequence the released DNA fragments.

Positive and Negative Control Antibodies

Utilize our Rabbit anti-Mouse Secondary Antibody to ensure efficient tethering of pA/G-MNase in the vicinity of your antigen. 

Rabbit anti-Mouse Secondary Antibody

The Rabbit anti-DYKDDDDK Antibody efficiently binds DYKDDDDK-tagged recombinant proteins and allows direct tethering of the pA/G-MNase fusion protein.

Rabbit anti-DYKDDDDK Primary Antibody

The Mouse anti-DYKDDDDK Antibody efficiently binds DYKDDDDK-tagged recombinant proteins and allows indirect tethering of the pA/G-MNase fusion protein in conjunction with the Rabbit anti-Mouse Secondary Antibody. 

Mouse anti-DYKDDDDDK Primary Antibody

Concanavalin A coated magnetic beads allow immobilization of living cells without affecting cell physiology while ensuring good sample retention through numerous wash steps to reduce background signal.

Concanavalin A Beads



Complementary Products available at antibodies-online:

antibodies-online™ Sets

We offer more than 1 million research antibodies, ELISA kits, proteins and related products from over 150 suppliers. This is a unique portfolio on the web. 

We help Scientists find the right product 

We want to provide transparency in the life science market and simplify the search for the correct product. To achieve this, we constantly work on the search function of By standardizing product data, we make the products on our website comparable. If a scientist has trouble finding the matching product, our scientific support team provides help.

About antibodies-online:

About us

We help Scientists find the right antibody

Benefit from antibodies-online years of expertise and accelerate your research with our CUT&RUN Sets and guidance to find the right antibody.

antibodies-online is the leading vendor-independent marketplace for research reagents, especially antibodies and ELISA kits. The company was founded in 2006 as a spin-off from RWTH Aachen University (Germany). We deliver research products to customers in over 70 different countries. We currently list over 1,95 million research products, which we deliver to universities, biotech and pharmaceutical companies worldwide.

Our diverse team consists of highly motivated biologists, IT- and business specialists. Together we strive to provide scientists with the best possible support for their research.

The successful execution of CUT&RUN hinges on antibody selection. In order to cut adjacent DNA, the pA/G-MNase fusion protein needs to recognize the targeted chromatin part. As is the case with ChIP, the success depends in large part on the affinity of the antibody for its target and its specificity under the conditions used for binding.

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Phone +49 (0)241 95 163 153  


57 rue d'Amsterdam
Paris 75008

Phone +33 (0)1 76 63 32 65 

United States

PO Box 5201
Limerick, PA 19468

Phone +1 877 302 8632 


CUTANA™ pAG-MNase for ChIC/CUT&RUN Assays

Recombinantly produced in E. coli, CUTANA™ pAG-MNase for ChIC/CUT&RUN Assays is a fusion of Proteins A and G to Micrococcal Nuclease. The pAG-MNase fusion enzyme may be used in conjunction with any of our CUT&RUN Product Sets.