Reliable and robust chromatin mapping assays

CUTANA™ ChIC / CUT&RUN assays leverage recent advancements in immunotethering technologies to deliver efficient, ultra-sensitive chromatin mapping capabilities. Compared to ChIP-seq, the leading assay for epigenomic profiling, CUT&RUN offers clear advantages:

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  • Extremely reliable, cost-effective workflow
  • Fewer cells required
  • Only 3-5 million reads required / sample
  • High signal : noise ratio
  • Diverse sample inputs and targets

CUTANA™ CUT&RUN offers distinct advantages vs. ChIP-seq, the standard chromatin mapping assay.

How does CUT&RUN work?

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 reads, significantly reducing sequencing costs vs ChIP-seq.

CUT&RUN has superior signal : noise with
> 10-fold reduced seq depth compared to ChIP-seq

CUT&RUN vs ChIP-Seq signal to noise comparison tracks

A representative 350 kb region of H3K4me1 profiles in K562 cells, generated using CUT&RUN (yellow tracks), native ChIP-seq (blue tracks), or cross-linked ChIP-seq (green tracks). All data were generated by EpiCypher and are expressed as reads per million (RPM). Color-coded gradient (to right) represents signal-to-noise ratios determined by genome-wide analysis (bamFingerprint data, not shown).

CUTANA™ CUT&RUN:
Go from cells to data in < 4 days

CUTANA CUT&RUN protocol timeline

Get started with CUTANA™ CUT&RUN assays

CUTANA™ pAG-MNase for ChIC / CUT&RUN

Design and execute your own CUT&RUN experiments with CUTANA pAG-MNase, the key reagent for CUT&RUN assays. Available for 50 or 250 reactions.

CUTANA ChIC/CUT&RUN Kit

Jumpstart your chromatin profiling assays with our 48 reaction CUT&RUN kits. Go from cells to isolated DNA using out robust, user-friendly workflow with built-in experimental controls.

CUTANA™ CUT&RUN Compatible Antibodies

SNAP-ChIP® certified, CUTANA-compatible antibodies are rigorously validated to ensure comparable results in ChIP-seq and CUT&RUN assays.

 

The CUTANA™ CUT&RUN Protocol

EpiCypher offers a collection of products for CUT&RUN assays, including pAG-MNase, spike-in controls, antibodies, and accessory reagents / tools, making it easy to create your own assay or follow a standard protocol.

We have developed a reliable and user-friendly CUT&RUN protocol, optimized for:

  • Diverse targets, including histone PTMs, transcription factors, and more
  • Low cell inputs (down to 5,000 cells)
  • Reduced sequencing depths (3-5 million reads)
  • Fresh, frozen, and cross-linked cells or nuclei

In addition, we have addressed common issues (e.g. bead clumping / loss) and enabled high-throughput sample handling via an 8-strip format. The protocol includes notes throughout, critical steps, pictures for clarity, and a FAQ section.

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Above is a comprehensive walkthrough video put together by our scientific and technical support team to compliment our CUT&RUN protocol.

View our Protocol

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