---
title: "How should nuclei look for CUTANA™ assays?"
slug: "how-should-nuclei-look-cut-and-tag"
updated: 2026-02-27T15:20:26Z
published: 2026-02-27T15:20:26Z
canonical: "support.epicypher.com/how-should-nuclei-look-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.

# How should nuclei look for CUTANA™ assays?

> This article also applies to meCUT&RUN and Multiomic CUT&RUN.

For nuclei preparations, >95% nuclei should be Trypan Blue positive or "dead" and unclumped. Nuclei should be round, intact, and contain minimal debris, as this could indicate lysis. Use [Trypan Blue staining](/v1/docs/trypan-blue-staining) to monitor and optimize nuclear extraction, increasing spin time if losing sample. See **Figure 1** for an example of high quality nuclei prep.

**Note:** To best ensure success, we suggest using our [nuclei extraction protocol](/v1/docs/nuclei-extraction-protocol-for-cutana-assays).

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

**Figure 1.** Morphology characteristic of intact K562 cells (left) compared to isolated nuclei (right) when visualized under brightfield microscope after Trypan Blue staining. Isolated nuclei will stain blue, while cells will be bright white and round. For accurate nuclei counts, record "dead" cell numbers on an automated cell counter or manually count blue stained nuclei.