CUT&Tag-IT™ Assay Kit

Rapid and robust genome-wide analysis of histone marks and transcription factor binding at lower sequencing depths


CUT&Tag-IT™ Assay Kit Overview

Cleavage Under Targets and Tagmentation (CUT&Tag) is a method to investigate genomic localization of histone modifications and some transcription factors that reveals interactions between proteins and DNA or identifies DNA binding sites for proteins of interest.

Unlike MNase-Seq or ATAC-Seq methods that target open chromatin and are therefore dependent on chromatin accessibility, CUT&Tag utilizes an antibody-based enzyme tethering strategy to target specific histone modifications or proteins to reveal chromatin-binding information that is specific to those sites or proteins of interest.

CUT&Tag is based on the same principles as ChIP-Seq, but with several changes to the protocol that are advantageous in certain situations. Instead of the sonication of fixed chromatin and immunoprecipitation steps performed in ChIP-Seq protocols, in CUT&Tag, fresh (not frozen) unfixed cells are bound to concanavalin A beads and the antibody incubation is performed with cells in their native state. Directly following antibody binding, the chromatin is digested and NGS libraries are prepared in a single step by tagmentation using the protein A-Tn5 (pA-Tn5) transposome enzyme that has been pre-loaded with sequencing adapters.

CUT&Tag can rapidly produce high-quality results from less starting material than ChIP-Seq, and enables robust analysis from lower sequencing depths, saving both time and money.

Learn more about CUT&Tag and how it works

CUT&Tag-IT™ Assay Kit Advantages:

  • Compatible with as few as 5,000 cells
  • Complete kit with optimized protocol
  • Developed for histone marks and some transcription factors
  • Sequencing-ready libraries without the laborious and costly steps of ChIP-Seq
  • Low background signal enables lower sequencing depth
  • No artifacts caused by formaldehyde crosslinking

How the CUT&Tag-IT™ Assay Works

How the Cut&Tag-IT™ Assay Works

FREE Antibody with Cut&Tag-IT™ Assay Kit Purchase

CUT&Tag vs. CUT&RUN vs. ChIP-Seq

  CUT&Tag-IT™ Assay Kit CUT&RUN ChIP-Seq
Performed Under Native Conditions? Yes Yes No
Chromatin Fragmentation Method Tn5-based tagmentation MNase digestion Sonication
Cell Number Requirements 5,000-500,000 cells 500,000 cells 1-10 million cells
Sequencing Depth Required * 2 million reads 8 million reads 20-50 million reads
Integrated Library Preparation? Yes, uses tagmentation No, separate library prep required No, separate library prep required
Compatible Targets Primarily histone modifications, some transcription factors and co-factors Wide range of histone modifications, transcription factors, and co-factors Wide range of histone modifications, transcription factors, and co-factors
Workflow Length 1-2 days 1-2 days 2-3 days

* Kaya-Okur et al. Nature Communications (2019) 10:1930


CUT&Tag-IT™ Assay Kit Contents

The CUT&Tag-IT™ Assay Kit components are shipped at two temperatures, with one box on dry ice for components to be stored at -20°C, and a second box at room temperature for components that are not to be frozen and must be stored at 4°C. Please store components according to the storage conditions in the manual after first use. All reagents are guaranteed stable for 6 months from date of receipt when stored properly.

Reagents included:

  • 5% Digitonin, store at -20°C
  • Concanavalin A Beads, store at 4°C
  • CUT&Tag-IT™ Assembled pA-Tn5 Transposomes, store at -20°C
  • Tagmentation Buffer, store at -20°C
  • 1X Binding Buffer, store at 4°C
  • 1X Wash buffer, store at 4°C
  • Dig-Wash Buffer, store at 4°C
  • Antibody Buffer, store at 4°C
  • Dig-300 Buffer, store at 4°C
  • Guinea Pig Anti-Rabbit Antibody, store at -20°C
  • Protease Inhibitor Cocktail, store at -20°C
  • 0.5M EDTA, store at RT
  • 10% SDS, store at RT
  • 10 µg/µL Proteinase K, store at -20°C
  • DNA Purification Columns, store at RT
  • DNA Purification Binding Buffer, store at RT
  • DNA Purification Wash Buffer, store at RT
  • DNA Purification Elution Buffer, store at RT
  • 3M Sodium Acetate, store at RT
  • 10 mM DNTPs, store at -20°C
  • 5X Q5 Buffer, store at -20°C
  • Q5 High Fidelity DNA Polymerase (2U/µL), store at -20°C
  • i5 Indexed Primer 1, store at -20°C
  • i5 Indexed Primer 2, store at -20°C
  • i5 Indexed Primer 3, store at -20°C
  • i5 Indexed Primer 4, store at -20°C
  • i7 Indexed Primer 1, store at -20°C
  • i7 Indexed Primer 2, store at -20°C
  • i7 Indexed Primer 3, store at -20°C
  • i7 Indexed Primer 4, store at -20°C
  • SPRI Beads, store at 4°C

Don’t forget to use an antibody validated for CUT&Tag!

Active Motif specializes in manufacturing high-quality antibodies to histones, histone modifications, chromatin proteins, and other factors, including a growing list of antibodies that we have experimentally validated in-house to work well in CUT&Tag assays. Check out our list of CUT&Tag-validated antibodies.

For a limited time, you can get a free antibody of your choice with every purchase of the CUT&Tag-IT™ Assay Kit. Learn more.


CUT&Tag-IT™ Assay Kit Data

CUT&Tag-IT™ Assay Kit compared with published data(Click image to enlarge)

Figure 1: CUT&Tag-IT Assay Kit data correlate well with ENCODE ChIP-Seq data.
Chromatin landscapes from human K562 cells are shown across a 868 kb segment of the human genome region (Chr16: 10,400-11,250) for H3K27me3 (dark blue), phospho-Pol2Ser2 (red), CTCF (orange), H3K4me3 (green), H3K9ac (light blue) H3K9me3 (purple), and H3K27ac (black) showing high concordance of CUT&Tag-IT Assay Kit signals from 100,000 cells compared with ENCODE ChIP-Seq data from at least one million cells. Antibodies used in the CUT&Tag assays for the following targets were: H3K27me3: cat. no 39155, CTCF: cat. no. 61311, H3K4me3: cat. no. 39159, H3K9ac: cat. no. 39917, H3K9me3: cat. no. 39161, H3K27ac: cat. no. 39133.



CUT&Tag-IT™ Assay Kit Documents




Order CUT&Tag-IT™ Assay Kit


We recommend using a CUT&Tag-validated antibody for best results. For a limited time, you can get a free antibody of your choice with every purchase of the CUT&Tag-IT™ Assay Kit. Learn more.

You might also be interested in:

US Pat. No. 10,689,643, EP Pat. No. 2999784 and related patents and applications

Name Format Cat No. Price  
CUT&Tag-IT™ Assay Kit 16 rxns 53160 $1,100 Buy
pA-Tn5 Transposase 10 µg 53161 Get Quote