---
title: "CUT&RUN Controls | Positive, Negative & Spike-in Controls"
slug: "what-controls-should-i-use-cut-and-run"
description: "Learn which positive, negative, and spike-in controls to use for CUT&RUN to validate assay performance and interpret results."
tags: ["cut and run"]
updated: 2024-10-01T16:25:51Z
published: 2024-10-01T16:25:51Z
canonical: "support.epicypher.com/what-controls-should-i-use-cut-and-run"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://support.epicypher.com/llms.txt
> Use this file to discover all available pages before exploring further.

# What control antibodies and spike-ins should I use in CUT&RUN?

EpiCypher has specific recommendations for control antibodies and spike-ins controls in CUT&RUN experiments, outlined below. Note that these controls are included in the CUTANA™ CUT&RUN Kit; for DIY CUT&RUN protocol users, links to relevant products are provided.

## **Control antibodies paired with SNAP-CUTANA™ K-MetStat Panel**

Reactions using negative control (IgG) and positive control (H3K4me3, H3K27me3) antibodies should be included in every experiment to validate protocols and examine assay background. When paired with the SNAP-CUTANA Spike-in K-MetStat Panel of nucleosome spike-in controls, control reactions can assist in [validating](/v1/docs/using-snap-cutana-spike-in-controls-to-determine-assay-success) and [troubleshooting](/v1/docs/using-snap-cutana-spike-ins-to-troubleshoot-workflows) your workflow.

- H3K4me3, [EpiCypher 13-0060](https://www.epicypher.com/products/antibodies/h3k4me3-antibody-snap-certified-for-cut-run-and-cut-tag)
- H3K27me3, [EpiCypher 13-0055](https://www.epicypher.com/products/antibodies/h3k27me3-antibody-snap-certified-for-cut-run-and-cut-and-tag)
- IgG, [EpiCypher 13-0042](https://www.epicypher.com/products/nucleosomes/snap-cutana-spike-in-controls/cutana-igg-negative-control-antibody-for-cut-run-and-cut-tag)
- SNAP-CUTANA K-MetStat Panel, [EpiCypher 19-1002](https://www.epicypher.com/products/nucleosomes/snap-cutana-k-metstat-panel)

## ***E. coli* Spike-in DNA for sequencing normalization**

*E. coli* DNA ([EpiCypher 18-1401](https://www.epicypher.com/products/nucleosomes/snap-cutana-spike-in-controls/cutana-e-coli-spike-in-dna)) is spiked in prior to library prep to aid in library prep and sequencing troubleshooting as well as normalization. For more information on how to use *E. coli* spike-in DNA for normalization, see [this article](/v1/docs/normalizing-to-e-coli-spike-in-dna).

## **Spike-in nucleosome controls for experimental targets**

[SNAP-CUTANA Spike-in Controls](https://www.epicypher.com/technologies/snap-spike-in-controls) are the only control that uses purified recombinant nucleosomes, replicating the physiological target of CUT&RUN assays. These panels of on- and off-target spike-ins can be used to validate antibodies to experimental targets, including lysine methylation PTMs and epitope-tagged proteins. For more information visit the [SNAP-CUTANA Spike-in section](/v1/docs/snap-cutana-spike-ins) or navigate to specific articles on:

- [What are SNAP-CUTANA Spike-in Controls and how do they work?](/v1/docs/what-are-snap-cutana-spike-ins-how-do-they-work)
- [Analyzing SNAP-CUTANA Spike-in Control Data](/v1/docs/analyzing-snap-cutana-spike-in-controls-and-expected-results)
- Using SNAP-CUTANA Spike-in Controls to [determine CUT&RUN success](/v1/docs/using-snap-cutana-spike-in-controls-to-determine-assay-success)
- Using SNAP-CUTANA Spike-in Controls to [troubleshoot workflows](/v1/docs/using-snap-cutana-spike-ins-to-troubleshoot-workflows) or [validate histone PTM antibodies](/v1/docs/using-snap-cutana-spike-in-controls-for-histone-ptm-antibody-validation)