---
title: "Why is there background in open chromatin in my CUT&Tag data?"
slug: "background-open-chromatin-cut-and-tag"
updated: 2024-12-04T14:12:58Z
published: 2024-12-04T14:12:58Z
canonical: "support.epicypher.com/background-open-chromatin-cut-and-tag"
---

> ## 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.

# Why is there background in open chromatin in my CUT&Tag data?

High background in CUT&Tag data can occur due to a preference of Tn5 for accessible chromatin. The high-salt wash after pAG-Tn5 binding helps reduce signal at open chromatin, but some background may be present in the IgG control and when profiling repressive targets. To minimize background:

- Use freshly harvested, native nuclei
- Always include the IgG negative control for comparison
- Confirm sample prep quality, as cell/nuclear lysis increases background. See the Sample Prep Section of this website for guidance on sample prep.