SKU: 14-1048
Pack size: 48 Reactions


The CUTANA™ ChIC/CUT&RUN Kit enables streamlined chromatin profiling of histone post-translational modifications (PTMs) and chromatin associated proteins while providing increased throughput and reproducibility with multi-channel pipetting.

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Positive (H3K4me3) and negative (IgG) control antibodies are included to pair with SNAP-CUTANA™ spike-in controls for assay optimization and continuous monitoring (Figure 2). E. coli DNA is included for data normalization. The kit is compatible with a variety of inputs including cells or nuclei derived from native, cryopreserved, or cross-linked samples. While it is recommended to start with 500,000 cells, comparable data can be generated using as few as 5,000 cells. The inclusion of controls and compatibility with diverse target types, sample inputs, and low cell numbers make this kit the go-to solution for chromatin mapping experiments. To place bulk orders, contact

Validation Data

Figure 1: CUT&RUN DNA Fragment Size Distribution Analysis
CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit starting with 500,000 K-562 cells. CUT&RUN DNA, isolated from IgG Negative Control (EpiCypher 13-0042k) and H3K4me3 Positive Control (EpiCypher 13-0041k) antibodies, was used to prepare paired-end Illumina sequencing libraries. Library DNA was analyzed by Agilent Tapestation®. This analysis confirmed that mononucleosomes were predominantly enriched in CUT&RUN (~300 bp peak represents 150 bp nucleosomes + sequencing adapters).

Figure 2: 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&RUN samples prior to the addition of the control antibodies provided with the kit (IgG, H3K4me3). Instances of each spike-in barcode 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) and H3K4me3 (bottom; normalized to on-target) antibodies provided with this kit are shown. The spike-ins confirmed optimal experimental conditions (H3K4me3 antibody specifically recovered the target dNuc, while IgG showed no preferential enrichment).

Figure 3: CUT&RUN genome-wide heatmaps
CUT&RUN data was generated using the CUTANA ChIC/CUT&RUN Kit with 500,000 K-562 cells. Three replicates (“Rep”) of IgG (left) and H3K4me3 (right) antibodies are shown in a heatmap. CUT&RUN signal (from an average of 5.9 million paired-end reads) aligned to the transcription start site (TSS, +/- 2kb) are presented for 18,793 genes. High and low signal are ranked by intensity (top to bottom) and reflected by red and blue colors, respectively. Gene rows in each heatmap are aligned and sorted from high to low signal relative to H3K4me3 Rep 3 (far right), demonstrating the reproducibility of the kit workflow.

Figure 4: Representative gene browser tracks
CUT&RUN data was generated as described in Figure 3. A representative 150 kb window at the TRMT2A gene is shown for three replicates (“Rep”) of IgG and H3K4me3 antibody controls (included in the kit). Representative tracks are also shown for H3K27me3 (EpiCypher 13-0030) and the transcription factor CTCF (EMD Millipore 07-729) antibodies. The CUT&RUN kit produced the expected genomic distribution for each target. Images were generated using the Integrative Genomics Viewer (IGV, Broad Institute).

Kit Contents

Item Cat. No.
CUTANA™ pAG-MNase for ChIC/CUT&RUN Workflows 15-1016
Histone H3K4me3 Antibody, SNAP-Certified™ for CUT&RUN and ChIP 13-0041k
CUTANA™ Rabbit IgG CUT&RUN Negative Control Antibody 13-0042k
SNAP-CUTANA™ K-MetStat Panel 19-1002k
CUTANA™ Concanavalin A Conjugated Paramagnetic Beads 21-1401
CUTANA™ E. coli Spike-in DNA 18-1401
CUTANA™ CUT&RUN 8-strip 0.2 mL Tubes 10-0009
Bead Activation Buffer 21-1001
Pre-Wash Buffer 21-1002
Stop Buffer 21-1003
5% Digitonin 21-1004
1 M Spermidine 21-1005
0.5 M EDTA 21-1006
100 mM Calcium Chloride 21-1007
DNA Cleanup Columns 10-0010
DNA Collection Tubes 10-0011
DNA Binding Buffer 21-1008
DNA Wash Buffer 21-1009
DNA Elution Buffer 21-1010

Recommended Accessory Products

Item Cat No.
CUTANA™ CUT&RUN Library Prep Kit 14-1001/14-1002
SNAP-CUTANA™ K-MetStat Panel 19-1002
CUT&RUN Antibodies See the list
Magnetic Separation Rack, 0.2 mL Tubes 10-0008
Magnetic Separation Rack, 1.5 mL Tubes 10-0012

Technical Information

Kit Contents
Kit contains buffers, enzymes, magnetic beads, control antibodies, spike-in controls, 8-strip tubes, and spin columns necessary to prepare and purify CUT&RUN DNA starting from cells or nuclei. See Kit Manual for additional materials and equipment required for the protocol.
Storage and Stability
OPEN KIT IMMEDIATELY and store components at room temperature, 4°C, and -20°C as indicated (see Kit Manual for full instructions). Stable for 6 months upon date of receipt.
Instructions for Use
See Kit Manual for complete instructions.

Documents & Resources

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