CUTANA™ ChIC/CUT&RUN Kit

Low inputs. Reduced costs. Superior data quality.

Product Description

Map histone post-translational modifications (PTMs) and chromatin-associated proteins, including transcription factors, with exceptional resolution and sensitivity.

CUTANA™ CUT&RUN advantages compared to ChIP-seq:

High signal-to-noise at reduced sequencing depth
Low cell input requirements
Diverse sample inputs and targets
Streamlined and cost-effective workflow

The CUT&RUN Kit Version 5 (v5) now includes an additional control antibody (H3K27me3). Positive (H3K4me3 and H3K27me3) and negative (IgG) control antibodies pair with SNAP-CUTANA™ spike-in controls for assay optimization and continuous assay monitoring (Figure 3). E. coli DNA is included for data normalization. SPRI magnetic beads are used for DNA purification, enabling seamless multi-channel pipetting throughout the workflow to maximize throughput and reproducibility.

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, as well as compatibility with diverse target types, sample inputs, and low cell numbers, make this kit the go-to solution for chromatin mapping experiments.

Questions?

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How does CUT&RUN work?

14 1048 V5 Cutarun Methods

Figure 1: CUT&RUN Workflow

The Cleavage Under Targets and Release Using Nuclease (CUT&RUN) method builds upon Chromatin ImmunoCleavage (ChIC) technology.

In CUT&RUN, a fusion of protein A, protein G and micrococcal nuclease (pAG-MNase) is used to selectively cleave antibody-labelled chromatin. This strategy eliminates immunoprecipitation steps, greatly simplifying the assay workflow. Clipped chromatin fragments are isolated from solution and used for NGS.

The targeted enrichment of CUT&RUN allows for better signal : noise with only 3-5 million sequencing reads, significantly reducing sequencing costs vs ChIP-seq.

Supporting Data

14 1048 V5 Dna Fragment Size Distribution

Figure 2: CUT&RUN DNA Fragment Size Distribution Analysis.
CUT&RUN was performed as described in Figure 1. Library DNA was analyzed by Agilent Tapestation®. This analysis confirmed that mononucleosomes were predominantly enriched in CUT&RUN (~300 bp peaks represent 150 bp nucleosomes + sequencing adapters).

14 1048 V5 Spike In Controls

Figure 3: SNAP-CUTANA™ K-MetStat Spike-in Controls.
DNA-barcoded designer nucleosomes (dNucs) harboring distinct K-methyl PTMs were spiked into CUT&RUN reactions prior to antibody addition. Spike-in barcodes were analyzed using the shell script available on the spike-in product page (EpiCypher 19-1002). Barcodes for IgG (normalized to total reads), H3K4me3 and H3K27me3 (normalized to on-target) antibodies are shown. The spike-ins confirmed H3K4me3 and H3K27me3 antibodies specifically recovered the target dNucs, while IgG showed no preferential enrichment.

14 1048 V5 Genome Wide Heatmaps

Figure 4: CUT&RUN genome-wide heatmaps.
CUT&RUN was performed as described in Figure 1. Heatmaps show two replicates (“Rep”) of IgG, H3K4me3, and H3K27me3 kit control antibodies in aligned rows ranked by intensity (top to bottom) relative to the H3K4me3 Rep 1 reaction and colored such that red indicates high localized enrichment and blue denotes background signal.

14 1048 V5 Representative Gene Browser Tracks

Figure 5: Representative gene browser tracks.
CUT&RUN was performed as described in Figure 1. A representative 175 kb window at the TRMT2A gene is shown for two replicates (“Rep”) of IgG, H3K4me3, and H3K27me3 kit control antibodies. Representative tracks are also shown for the transcription factor CTCF. The CUT&RUN kit produced the expected genomic distribution for each target. Images were generated using the Integrative Genomics Viewer (IGV, Broad Institute).