---
title: "How to Optimize CUT&RUN Assays | Best Practices & Tips"
slug: "optimize-cut-and-run-targets-cells"
description: "Optimize CUT&RUN assays with best practices for sample preparation, antibodies, digestion, library prep, sequencing, and data quality."
tags: ["cut and run"]
updated: 2024-10-01T16:12:07Z
published: 2024-10-01T16:12:07Z
canonical: "support.epicypher.com/optimize-cut-and-run-targets-cells"
---

> ## 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 optimize CUT&RUN for new targets, cell types, or low cell numbers

For new targets and cell types, optimize CUT&RUN workflows as described in **Figure 1**. CUT&RUN success depends on many factors, including cell type, cell number, target abundance, and antibody quality.

Note that using low cell numbers may result in lower signal and increased background, including for control antibodies. Lower yields may be partly due to antibody quality and target abundance, as well as reduced cell numbers. Furthermore, an antibody that works well with 500,000 cells may fail at lower inputs. Library prep can be [optimized for low yields](/v1/docs/cut-and-run-library-prep-low-yields). Deeper sequencing is often recommended.

![optimization CUTRUN updated](https://cdn.document360.io/1fc69f91-cf1e-45ab-bc51-4063eb80e37c/Images/Documentation/optimization%20CUTRUN%20updated.png)

**Figure 1.** Development and optimization guides for successful CUT&RUN workflows.