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Expires 31 August 2026

CUTANA CUT&Tag Kit (Primer Set 1 Subset)

Ultra Low Input Chromatin Mapping Assay

Product Description

Map histone post-translational modifications (PTMs) with exceptional sensitivity and low background, even from limited cell numbers.

CUTANA™ CUT&Tag advantages compared to ChIP-seq

Fast: Cells to sequencing in 2 days
Streamlined: Exclusive single-tube protocol, no library prep
High Sensitivity: Reliable data down to 10,000 cells
Scalable: Designed for multi-channel pipetting and 8-strip tubes
Dramatic cost savings: Only 5-8 million sequencing reads

In CUT&Tag, antibody-bound chromatin is selectively cleaved with fusion protein pAG-Tn5, which simultaneously adds sequencing adapters.

Go from cells to PCR-amplified sequencing libraries in one tube with minimal sample loss.Tagmented fragments bypass traditional library prep with CUTANA™ CUT&Tag Kit’s exclusive Direct-to-PCR strategy.

Generate comparable data down to 10,000 nuclei. The protocol is also validated for whole cells, cryopreserved samples, and lightly cross-linked nuclei or cells.

The CUT&Tag Kit Version 4 (v4) now includes two new Wash Buffer Enhancers, CUTANA™ DNA Purification beads, and improvements to the CUT&Tag protocol. CUTANA™ DNA Purification Beads are optimized for high yield DNA clean up with precise size selection, while the CUTANA™ Wash Buffer Enhancers reduce clumping and improve bead handling. Protocol improvements amplify sample preservation with changes to nuclei resuspension and refine reaction handling to increase yields for difficult targets. The protocol is also designed for compatibility with multi-channel pipetting for increased throughput and reproducibility. Positive (H3K4me3 and H3K27me3) and negative (IgG) control antibodies are paired with the SNAP-CUTANA™ K-MetStat Panel of nucleosome spike-in controls (Figure 2) to continuously monitor workflows and guide troubleshooting. CUTANA™ CUT&Tag Kits are bench-tested, scientist-approved, providing users with quality reagents for precision mapping.

Recommendations for Usage

CUT&Tag provides robust profiling for histone PTMs.

For chromatin-associated proteins (e.g. transcription factors), CUTANA™ CUT&RUN is recommended (CUT&RUN Kit plus CUT&RUN Library Prep).

Questions?

Connect with us today to get started on your CUT&Tag workflow.

How does CUT&Tag work?

Cut And Tag Workflow

Figure 1: CUT&Tag Workflow

Multiplexed Primers

The CUTANA Cut & Tag Kit is available with two different primer sets. Each kit contains combinatorial dual indices for multiplexed sequencing of up to 48 reactions. Customers can combine the kits to multiplex up to 96 reactions:

CUTANA CUT&Tag Kit Version 4, Primer Set 1 (Cat.# 14-1102-48s1-EPC)
CUTANA CUT&Tag Kit Version 4, Primer Set 2 (Cat.# 14-1102-48s2-EPC)
CUTANA CUT&Tag Kit Version 4, Primer Set 1 Subset (Cat.# 14-1102-24s3-EPC)

Included Reagents

pAG-Tn5 for targeted chromatin tagmentation
ConA magnetic beads for immobilizing cells/nuclei
SNAP-CUTANA™ Spike-in Controls for assay optimization and reaction monitoring
Positive (H3K27me3, H3K4me3) and negative (IgG)
Anti-Rabbit Secondary Antibody
i5 and i7 primers, PCR Master Mix, and SPRI beads for indexing PCR and library purification
8-strip tubes, multiplexing primers, buffers, buffer components

Learn more about the CUT&Tag Technology

Supported Applications

Related Products

Individual core reagents and antibodies for CUTANA CUT&Tag Assays are also available.

Supporting Data

14 1102 V4 Distribution Analysis Fig2

Figure 2: CUT&Tag DNA fragment size distribution analysis. CUT&Tag was performed as described in Figure 1. Library DNA was analyzed by Agilent TapeStation®, which confirmed that mononucleosomes were predominantly enriched in CUT&Tag (peak between 300-400 bp). Peak between 500-700 bp represents dinucleosomes.

14 1102 V4 Spike In Controls Fig3

Figure 3: SNAP-CUTANA™ K-MetStat Spike-in controls. DNA-barcoded designer nucleosomes (dNucs) representing 16 different K-methyl PTM states: mono-, di-, and tri-methylation at H3K4, H3K9, H3K27, H3K36, and H4K20, as well as unmodified control, were spiked into CUT&Tag samples prior to the addition of the control antibodies provided with the kit (IgG, H3K27me3, H3K4me3). After sequencing, instances of each spike-in barcode recovered in the CUT&Tag reactions were counted and normalized from raw fastq files using the shell script and analysis Excel sheet available on the spike-in product page (EpiCypher 19-1002). Barcodes for IgG (top; normalized to the sum of total reads), H3K27me3 (middle; normalized to on-target), and H3K4me3 (bottom; normalized to on-target) antibodies provided with this kit are shown. The spike-ins confirmed optimal experimental conditions (H3K27me3 and H3K4me3 antibodies specifically recovered the target dNuc, while IgG showed no preferential enrichment).

14 1102 V4 Genome Wide Heatmaps Fig4

Figure 4: CUT&Tag genome-wide heatmaps. CUT&Tag was performed as described in Figure 1. Heatmaps show two replicates (“Rep”) of IgG and H3K4me3 antibodies in aligned rows ranked by intensity (top to bottom) relative to the H3K4me3 Rep 1 reaction. High, medium, and low intensity are shown in red, yellow, and blue, respectively. Antibodies to histone PTMs showed expected enrichment patterns and high reproducibility. H3K4me3, a marker of active transcription localized to transcription start sites (TSSs), shows enrichment consistent at TSSs, as expected. IgG shows low background enrichment.

14 1102 V4 Gene Browser Tracks Fig5

Figure 5: Representative gene browser tracks. CUT&Tag was performed as described in Figure 1. A representative 186 kb window at the LAMC3 gene is shown for two replicates (“Rep”) of IgG, H3K27me3, and H3K4me3 kit control antibodies. Representative tracks are also shown for two replicates of H3K4me1 antibody. The CUT&Tag kit produced the expected genomic distribution for each target. Images were generated using the Integrative Genomics Viewer (IGV, Broad Institute).