---
title: "Expected CUT&RUN DNA Yields | Yield Guidelines & QC"
slug: "cut-and-run-yields"
description: "Learn the expected DNA yields for CUT&RUN experiments and how yield varies by target, sample type, and overall assay performance."
updated: 2024-10-01T16:23:15Z
published: 2024-10-01T16:23:15Z
canonical: "support.epicypher.com/cut-and-run-yields"
---

> ## 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 are typical DNA yields from CUT&RUN?

**There is** **no typical DNA yield for CUT&RUN**, as yields can vary by cell type, number of cells, target abundance, and antibody quality. We suggest the following metrics:

- Yields from the H3K4me3 control should be similar to or slightly greater than the IgG negative control.
  - Note that similar and/or low yields from the positive control reflect the low abundance of H3K4me3 and do NOT imply assay failure. Read more [here](/v1/docs/my-yields-from-the-h3k4me3-positive-control-are-low-ie-below-5-ng-about-the-same-as-the-igg-negative-control-did-my-experiment-fail).
- Yields from the H3K27me3 controls should be greater than IgG. This is due to higher abundance of H3K27me3 on chromatin.
- Aim for ≥5 ng CUT&RUN-enriched DNA, which will enable robust library prep.
  - Yields below 5 ng are common for low abundance targets, such as H3K4me3. In these cases, we suggest using all of the CUT&RUN DNA for library prep.
- For more help with low yields, see [this article](/v1/docs/what-should-i-do-if-i-have-low-cut-and-run-yields) and review [Basic Troubleshooting Guidelines](/v1/docs/troubleshooting-cut-and-run). Note that sometimes low yields cannot be avoided, but modifications can be made to library prep to increase yields for sequencing.

**Important note:** Do NOT assess fragment size distribution of CUT&RUN DNA. Raw CUT&RUN yields are too low for detection on Bioanalyzer/TapeStation, and will not provide useful information at this step. Wait until after library prep. For further reading, see [this FAQ](/v1/docs/qpcr-or-bioanalyzertapestation-to-evaluate-raw-cutrun-dna).