AVAILABLE PRODUCTS

CUT&Tag-IT® Assay Kit - Cells

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

 

CUT&Tag-IT® Assay Kit - Cells Overview

CUT&Tag-IT Assay KitCUT&Tag-IT® Assay Kit
CUT&Tag-IT Assay Core KitCUT&Tag-IT® Core Assay Kit
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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.

CUT&Tag-IT® Kit Selection Guide

Kit All Steps through NGS library creation Loaded pA-Tn5 Transposase CUT&Tag Assay Buffers
CUT&Tag-IT Assay Kit, Anti-Rabbit ✓ ✓ ✓
CUT&Tag-IT Assay Kit, Anti-Mouse ✓ ✓ ✓
CUT&Tag-IT Core Assay Kit ✗ ✓ ✓

CUT&Tag-IT® Assay Kit Advantages:

  • Compatible with as few as 5,000 cells
  • Complete kit with optimized protocol (excluding CUT&Tag-IT Core Assay Kit)
  • 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<sup>®</sup> Assay Works

Learn more about how CUT&Tag works

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

  CUT&Tag 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

** For less abundant targets of interest, 8 to 10 million reads are recommended

† 25 million reads are recommended for transcription factor targets

CUT&Tag Workshops
 

CUT&Tag-IT® Assay Kit - Cells 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.

Anti-Rabbit and Anti-Mouse Kits

Reagents included:

  • Alpaca Anti-Rabbit IgG (H+L), store at -20°C (only included in the Anti-Rabbit Kit, Cat Nos. 53160 and 53171)
  • Rabbit Anti-Mouse Antibody, store at -20°C (only included in the Anti-Mouse Kit, Cat Nos. 53165 and 53172)
  • 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 or 4°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
  • 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

Core Assay Kit

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 or 4°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
  • Rabbit Anti-Mouse Antibody, store at -20°C
  • Alpaca Anti-Rabbit IgG (H+L), 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

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.

 

CUT&Tag-IT® Assay Kit - Cells Data

CUT&Tag-IT<sup>®</sup> 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 - Cells FAQs

1. About CUT&Tag and When to Use It

CUT&Tag is a native, antibody-guided tagmentation method that profiles chromatin binding sites without fixation, sonication, or immunoprecipitation. Compared to ChIP-seq, CUT&Tag requires fewer cells, produces lower background, and generates sequencing-ready libraries in a single step.

  • No crosslinking: Performed in native cells
  • No sonication: Chromatin is cleaved by tethered pA-Tn5
  • Lower input: Works with fewer starting cells
  • Integrated library prep: Tagmentation generates sequencing-ready DNA
  • Lower background: Higher signal-to-noise than ChIP-seq
  • Lower sequencing depth: Fewer reads needed for robust results

These advantages make CUT&Tag-IT ideal for limited samples, rapid workflows, and cost-effective chromatin profiling.

Choose CUT&Tag when you have limited starting material and want high-resolution, low-background profiling of histone modifications or selected chromatin-associated proteins. CUT&Tag-IT is especially well suited for native cells, rapid workflows, and low sequencing depth.

  • Best for: Histone marks and chromatin features
  • Sample input: Low cell numbers
  • Signal quality: High signal-to-noise, low background
  • Workflow: Fast, integrated library preparation

For comprehensive analysis of genome-wide transcription factor binding—particularly for difficult or low-abundance targets—traditional ChIP-seq may still be preferred.

2. Kit Contents & General Compatibility

Yes. The CUT&Tag-IT® Assay Kit includes all core reagents required to perform CUT&Tag, including the pre-assembled protein A–Tn5 (pA-Tn5) transposomes loaded with sequencing adapters.

  • Included: pA-Tn5 transposomes, buffers, and reaction components
  • Not included: Standard laboratory equipment and general reagents
  • Documentation: A complete list of additional materials is provided in the kit manual

The only items not supplied are standard lab consumables and instruments, which are listed under Additional Materials Required in the CUT&Tag-IT® Assay Kit manual.

No. The standard Active Motif ChIP-Seq Spike-In Normalization method is not compatible with the CUT&Tag-IT® Assay Kit.

CUT&Tag-IT uses a targeted, antibody-tethered tagmentation approach that does not support external spike-in controls designed for ChIP-Seq workflows.

No. CUT&Tag-IT does not require an INPUT control.

Unlike ChIP-Seq, CUT&Tag uses a tethered pA-Tn5 transposase that targets DNA only at antibody-bound sites. This targeted mechanism eliminates the need for an INPUT control to normalize background signal.

3. Sample Input & Preparation

The recommended input for the CUT&Tag-IT® Assay Kit – Cells is 50,000 to 100,000 cells per reaction. Useful CUT&Tag data can also be generated from as few as 5,000 cells, depending on target abundance and antibody performance.

  • Recommended range: 50,000 – 100,000 cells
  • Minimum demonstrated input: ~5,000 cells
  • Performance depends on: Target abundance and antibody quality

Lower input experiments may require careful optimization and appropriate positive controls to ensure robust results.

Prepare cells exactly as described in the CUT&Tag-IT® manual. Cells must remain unfixed and viable.

For adherent cells, do not use trypsin, as it damages the surface epitopes required for binding to Concanavalin A beads.

  • Use enzyme-free dissociation
  • Scrape cells or use a rubber policeman
  • Avoid harsh mechanical or enzymatic treatments

Yes—if the cells were cryopreserved. Flash-frozen cell pellets are not compatible with the CUT&Tag-IT workflow.

  • Use cryopreserved cells only
  • Do not use flash-frozen pellets
  • Thaw gently and handle as described in the protocol

To cryopreserve cells correctly, follow Active Motif’s Services sample preparation protocol.

Concanavalin A (Con A) beads should appear evenly suspended and uniformly opaque. When cells bind, the beads become visibly larger, darker, and form soft aggregates that move together in the tube.

  • Unbound beads: fine, evenly dispersed particles
  • Cell-bound beads: larger clusters that settle more quickly
  • Clumping or debris: indicates poor cell prep or bead handling

Watch the short video below for a visual reference of proper bead appearance and binding:

4. Controls, QC & Data Quality

Use H3K27me3 as the technical positive control and a no-primary-antibody sample as the negative control.

  • Positive control: H3K27me3 antibody (Cat. No. 39157) — confirms reagent performance and workflow integrity
  • Negative control: Secondary antibody only (no primary) — measures background from pA-Tn5 and the secondary antibody

These controls verify assay specificity and help distinguish true signal from background noise.

No—an IgG control is not required for CUT&Tag-IT.

CUT&Tag uses a tethered pA-Tn5 enzyme that is highly specific for antibody-bound genomic regions. Internal testing by Active Motif showed that an IgG control does not add meaningful information beyond the standard negative control.

  • IgG controls are not used in downstream analysis
  • IgG controls are not equivalent to INPUT controls used in ChIP-Seq
  • Optional only if required for internal validation

Yes—library quality and concentration should always be checked before sequencing.

  • Size distribution: Analyze libraries on a TapeStation or Bioanalyzer. Most fragments should be < 500 bp.
  • Library concentration: Quantify using a KAPA Library Quantification Kit.

These QC steps ensure high-quality sequencing data and reduce the risk of failed runs.

5. Antibodies & Target Compatibility

Active Motif provides a curated list of antibodies validated specifically for CUT&Tag-IT.

View the full list of CUT&Tag-IT–validated antibodies here: CUT&Tag-validated antibodies

These antibodies have been tested for performance, specificity, and reproducibility with the CUT&Tag-IT workflow.

Not always. CUT&Tag and ChIP-Seq use very different workflows and binding conditions.

An antibody that performs well in ChIP-Seq does not necessarily work in CUT&Tag-IT. For reliable results, we recommend:

Antibody compatibility is one of the most important factors for successful CUT&Tag experiments.

Yes. The CUT&Tag-IT® Assay Kit is compatible with both monoclonal and polyclonal antibodies.

The assay supports antibodies raised in mouse or rabbit, which bind efficiently to the pA-Tn5 transposome used in the CUT&Tag-IT workflow.

Tagged proteins have not been formally validated with CUT&Tag-IT.

However, in principle, CUT&Tag-IT should work with tagged proteins if a high-quality antibody against the tag is used. Performance may vary, so validation with your specific tag and target is recommended before running large experiments.

6. Indexing, Multiplexing & qPCR

Yes. The CUT&Tag-IT® Assay Kit includes 4×4 unique dual indexes for multiplexing up to 16 samples.

To multiplex more than 16 samples (up to 96), use Active Motif’s Nextera™-Compatible Multiplex Primers (96-plex, Cat. No. 53155).

These primers match Illumina Nextera index sets (N701–N704 and N501–N504) and are supplied at 25 µM for direct use. You may also combine other Nextera-compatible primers at the same concentration.

Yes, but with important limitations. CUT&Tag-IT libraries can be analyzed by qPCR, however the results may be unreliable.

Because Tn5 inserts sequencing adapters at random positions, many fragments will not contain both primer binding sites. As a result, gene-specific qPCR primers may fail to amplify all target fragments.

Implication: qPCR can underestimate library abundance or target enrichment and should not be used as a quantitative replacement for sequencing.

They are dual-indexed.

Each CUT&Tag-IT library contains two unique index sequences (i7 and i5), enabling accurate sample demultiplexing and reducing index hopping on Illumina platforms.

No. CUT&Tag-IT libraries do not include molecular identifiers (UMIs).

Duplicate reads should be handled using standard alignment and duplicate-removal tools rather than UMI-based collapsing.

7. Sequencing & Bioinformatics

Paired-end sequencing is recommended.

Paired-end reads improve fragment mapping accuracy, peak resolution, and alignment confidence for CUT&Tag data.

We recommend paired-end 2 × 38 bp (PE38).

Although this is shorter than the read length reported in the original Henikoff CUT&Tag paper, Active Motif has not observed reduced mapping rates or data quality with PE38.

Longer read lengths may also be used if desired.

CUT&Tag data is analyzed using standard ChIP-Seq bioinformatics workflows.

Active Motif recommends aligning reads with BWA and performing peak calling with MACS2.

Downstream analysis (signal tracks, peak annotation, and differential binding) can be performed using the same tools and pipelines commonly used for ChIP-Seq datasets.

Questions about sample library QC? Read more on our blog.

Free CUT&Tag eBook


 

CUT&Tag-IT® Assay Kit - Cells Publications

Search our database of customer publications that have used our CUT&Tag-IT® Assay Kit for Cells.

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CUT&Tag-IT® Assay Kit - Cells Documents

 

You might also be interested in:

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

Permitted Use; Resale Prohibited

In the absence of an express written agreement to the contrary, all products are sold and services deliverables are provided by Active Motif for (a) internal in vitro research purposes only and may not be used for services or any other commercial purpose (b) the exclusive use of the original purchaser, and are not to be resold. You agree not to reverse engineer or otherwise attempt to discover the structure or composition of products or services deliverables unless we otherwise agree in writing.

 
Name Format Cat No. Price  
CUT&Tag-IT® Assay Kit, Anti-Rabbit 16 rxns 53160 $1,480 Add to Cart
3 x 16 rxns 53171 $3,090 Add to Cart
CUT&Tag-IT® Assay Kit, Anti-Mouse 16 rxns 53165 $1,480 Add to Cart
3 x 16 rxns 53172 $3,090 Add to Cart
CUT&Tag-IT® Core Assay Kit 16 rxns 53176 $745 Add to Cart
Counting Cells and Nuclei for Epigenetic Applications
CUT&Tag-IT® Assay Kit, Anti-Mouse Manual [Chinese]
CUT&Tag-IT® Assay Kit, Anti-Mouse Manual [English]
CUT&Tag-IT® Assay Kit Manual (with Alpaca Anti-Rabbit IgG 106706) [English]
CUT&Tag-IT® Core Assay Kit Manual (with Alpaca Anti-Rabbit IgG 106706)
CUT&Tag-IT® Core Assay Kit Manual (with Guinea Pig Anti-Rabbit Antibody 105465)
CUT&Tag-IT® Assay Kit Manual (with Guinea Pig Anti-Rabbit Antibody 105465) [Chinese]
CUT&Tag-IT® Assay Kit Manual (with Guinea Pig Anti-Rabbit Antibody 105465) [English]