Ultra low input chromatin mapping assays

CUTANA™ CUT&Tag assays build on recent advancements in immunotethering technology to deliver an innovative workflow to profile histone PTMs using < 5,000 cells.

CUT&Tag is an emerging technology with protocols in active development, including single cell workflows. This approach is ideal when profiling histone PTMs using < 5,000 nuclei or cells. For most experiments, EpiCypher strongly recommends using our robust CUTANA™ CUT&RUN assays, which is compatible with 5,000 to 500,000 cells and has been optimized for a wide range of targets, sample inputs, fixation conditions.

* CUT&Tag is not recommended for chromatin associated proteins – Use CUTANA CUT&RUN assays instead.

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Cut And Tag Video

CUTANA™ CUT&Tag provides impressive gains in histone PTM mapping compared to ChIP-seq, the leading chromatin mapping assay.

How does CUT&Tag work?

Cleavage Under Targets and Tagmentation (CUT&Tag) is a novel immunotethering assay, based on Cleavage Under Targets and Release Using Nuclease (CUT&RUN) method.

In CUT&Tag, a fusion of protein A, protein G, and Tn5 transposase is used to catalyze simultaneous cleavage and sequencing adapter ligation at antibody-bound chromatin. The use of Tn5 in CUT&Tag is a key advance, as this step eliminates the need for chromatin fragmentation as well as library preparation.

CUT&Tag assays display significantly improved signal-to-noise (S/N) vs. ChIP-seq assays, particularly for mapping histone PTMs in ultra-low sample inputs.

Quality PTM mapping with low input and sequencing depth requirements


CUTANA™ CUT&Tag generates similar results at a fraction of the cell input and sequencing depth used in ChIP-seq. A representative 300 kb region at the LAMC3 gene is shown for CUT&Tag (orange), CUT&RUN (green) and ChIP-seq (blue) data generated using H3K4me3 and H3K27me3 antibodies (EpiCypher 13-0041 and 13-0030, respectively). Rabbit IgG Negative Control Antibody (EpiCypher 13-0042) and ChIP Input control are shown for comparison (control tracks are scaled to the track with the highest signal in each approach).

Go from cells to sequencing-ready DNA in < 2 days

Get started with CUTANA™ CUT&Tag assays

CUT&Tag Core Reagents Bundle

Save 30% by bundling all your reagents together! This bundle has key reagents you will need including positive, negative, and spike-in controls.

CUT&Tag Accessory Products

We offer a wide range of companion products, including antibodies, beads, and more!

CUTANA™ pAG-Tn5 for CUT&Tag

Plan your next CUT&Tag experiment! pAG-Tn5 is the essential enzyme for CUT&Tag assays. Available in 50 or 250 reaction sizes.

The CUTANA™ CUT&Tag Protocol : Ideal Applications

In addition to pAG-Tn5, EpiCypher offers many supporting products to help you get started with CUT&Tag assays, such as antibodies, experimental controls, magnetic beads, and more!

As noted above, CUT&Tag is a new technology, and internal protocols are being updated regularly. Our latest version is validated for CUT&Tag assays mapping histone PTMs from as few as 1,000 nuclei/cells.

Of note, when mapping PTMs using >5,000 cells, or for profiling chromatin-associated proteins (at any input), we strongly recommend researchers use CUTANA™ CUT&RUN assays. Read our blog to learn more!

The CUT&Tag protocol also contains a thorough FAQ section, in which we address the most common questions about the CUT&Tag assay. For more information on our protocol and how to set up your own assay, read our blog and our CUTANA CUT&Tag brochure.

Kaya-Okur et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Comm. 10, 1930 (2019). (PMID: 31036827)

This paper introduces CUT&Tag methodology, as developed by the Henikoff laboratory at the Fred Hutchinson Cancer Research Center. It describes how the Tn5 fusion proteins works, demonstrates the application of CUT&Tag for histone PTM and chromatin factor profiling, and reveals major advantages of this new technology. Specifically, they use CUT&Tag to generate high-quality histone PTM profiles from single cells, a major advancement for the epigenetics field.

Kaya-Okur et al. Efficient low-cost chromatin profiling with CUT&Tag. Nat. Protoc. 15, 3264-3283 (2020). (PMID: 32913232)

Here, the inventors of CUT&Tag provide a highly detailed description of their optimized CUT&Tag protocol, citing EpiCypher’s pAG-Tn5 as the suggested commercial vendor of the enzyme. The protocol highlights critical steps, includes a troubleshooting FAQ table, and shows example results.

Henikoff et al. Efficient transcription-coupled chromatin accessibility mapping in situ. by nucleosome-tethered tagmentation. Elife 16;9:e63274.(2020). (PMID: 33191916)

In a paper from the inventors of CUT&RUN / CUT&Tag technology, they leveraged EpiCypher’s pAG-Tn5 and CUT&RUN compatible histone PTM antibodies to develop a modified version of CUT&Tag for chromatin accessibility mapping. Importantly, this new method generates robust, high-quality profiles using only 3-5M reads/samples (vs. 20-30M reads for standard ATAC-seq).