---
title: "How Many E. coli Spike-in Reads Do I Need for CUT&RUN?"
slug: "reads-for-e-coli-dna"
description: "Learn how many E. coli spike-in reads are needed for reliable CUT&RUN normalization and how to optimize spike-in DNA levels."
updated: 2025-12-17T15:00:02Z
published: 2025-12-17T15:00:02Z
canonical: "support.epicypher.com/reads-for-e-coli-dna"
---

> ## 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 many reads do I need for E. coli Spike-in DNA?

Aim for *E. coli* Spike-in DNA ([EpiCypher 18-1401](https://www.epicypher.com/product/cutana-e-coli-spike-in-dna/)) to comprise ~1% (0.2-5%) of total sequencing reads. In the protocol, 0.5 ng is recommended for 500,000 cells. Generally, this can be decreased linearly with decreasing cell number (e.g. 0.1 ng per 100,000 cells). The amount may need to be adjusted to achieve read counts in the optimal range due to variables such as target abundance, antibody efficiency, etc.

For more on *E. coli* optimization, see [this article](/v1/docs/optimizing-e-coli-spike-in-dna), and for more on normalizing to *E. coli* reads, see [this article](/v1/docs/normalizing-to-e-coli-spike-in-dna).