---
title: "How to Validate Chromatin Protein Antibodies for CUT&RUN"
slug: "cut-and-run-validate-a-chromatin-protein-antibody"
description: "Learn how to validate chromatin protein antibodies for CUT&RUN using positive controls, specificity testing, and sequencing results."
tags: ["cut and run"]
updated: 2026-02-27T15:25:43Z
published: 2026-02-27T15:25:43Z
canonical: "support.epicypher.com/cut-and-run-validate-a-chromatin-protein-antibody"
---

> ## 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.

# How to validate antibodies for chromatin protein targets

> This article also applies to Multiomic CUT&RUN.

We recommend selecting the antibody that best balances the need for robust DNA yields, enrichment for expected sequence motifs and/or peak structures, and high signal over background. Testing native and lightly cross-linked cell samples is also ideal for protein targets.

EpiCypher offers [CUT&RUN antibodies](https://www.epicypher.com/antibodies-complete-list/) to diverse chromatin-associated proteins, including transcription factors, chromatin reader proteins, chromatin modifying enzymes, remodelers, and commonly used epitope tags.

Can't find the antibody you need? Follow the steps below or [contact us](https://www.epicypher.com/contact-us/) for recommendations.

1. **Obtain 3-5 antibodies (preferably monoclonal) to your protein from various vendors.** Make sure that the antibodies target distinct epitopes.
  - EpiCypher scientists have observed that antibodies good for immunofluorescence (IF) applications tend to produce good data in our CUTANATM CUT&RUN assays. Although using IF-validated antibodies is **NOT** a guarantee for success, it may help guide CUT&RUN antibody selection for targets that lack validated reagents.
2. **Perform CUT&RUN with all candidate antibodies.**
  - Always include reactions with [H3K4me3](https://www.epicypher.com/products/antibodies/h3k4me3-antibody-snap-certified-for-cut-run-and-cut-tag) and [H3K27me3](https://www.epicypher.com/products/antibodies/h3k27me3-antibody-snap-certified-for-cut-run-and-cut-and-tag) positive control antibodies and [IgG](https://www.epicypher.com/products/nucleosomes/snap-cutana-spike-in-controls/cutana-igg-negative-control-antibody-for-cut-run-and-cut-tag) negative control antibodies. Add the [SNAP-CUTANA K-MetStat Panel](https://www.epicypher.com/products/nucleosomes/snap-cutana-k-metstat-panel) to control reactions to gauge experimental success.
3. **Confirm positive and negative controls show expected sequencing results, including data from the SNAP-CUTANA K-MetStat Panel.**
  - The negative controls should have low, nonspecific recovery of nucleosomes from the K-MetStat Panel, while the positive control reaction should only recover spike-in nucleosomes carrying the target PTM (e.g. H3K4me3 with less than 20% cross-reactivity to off-targets).
  - Positive controls should also generate robust peaks in expected genomic regions (i.e. sharp peaks at active transcription start sites for H3K4me3).
  - See an expanded discussion and example data [here](/v1/docs/analyzing-snap-cutana-spike-in-controls-and-expected-results).
4. **Examine sequencing data.** Select antibodies that generate high signal-to-noise in CUT&RUN and generate genomic distribution profiles consistent with the reported function of the target protein (for example, DNA binding motif analysis for transcription factors).