---
title: "Trypan blue staining protocol"
slug: "trypan-blue-staining"
description: "Learn how to use Trypan Blue staining to assess cell viability and evaluate sample quality before CUTANA™ CUT&RUN and CUT&Tag assays."
updated: 2026-09-02T02:15:10Z
published: 2026-09-02T02:15:10Z
canonical: "support.epicypher.com/trypan-blue-staining"
---

> ## 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.

# Trypan blue staining protocol

> [!NOTE]
> This article applies to CUT&RUN, meCUT&RUN and Multiomic CUT&RUN.
> 
> Important Notes
> 
> Trypan Blue is toxic to cells. After adding Trypan Blue dye to cells, move quickly to determine cell viability.

## **Materials needed**

| **Reagent** |
| --- |
| Trypan blue solution, 0.4% (e.g. Invitrogen T10282) |
| Hemocytometer with brightfield/phase microscope or automated cell counter (e.g.) Countess automated cell counter) |

## **Protocol**

1. Add 10 µL of 0.4% trypan blue to 10 µL washed cells/nuclei. Pipette to mix.
2. Transfer 10 µL of cell-trypan nlue mix to a counting slide.
3. View under brightfield/phase microscope or cell counter.
4. Assess cell/nuclei morphology and viability and troubleshoot as needed.
5. Viable cells are impermeable to trypan blue and will exclude the dye (trypan blue negative; **Figure 1A**).
  - Dead cells are permeable to trypan blue and will stain trypan blue positive (**Figure 1A**).
  - Isolated nuclei will stain trypan blue positive (**Figure 1B**).

![trypanBlue_ABonly_compressed(1)](https://cdn.document360.io/1fc69f91-cf1e-45ab-bc51-4063eb80e37c/Images/Documentation/trypanBlue_ABonly_compressed(1).png)**Figure 1.** (**A**) Washed K562 cells are mostly viable (bright white and round). A dead cell (blue, trypan positive) is circled in red. (**B**) Successful nuclei harvest shows trypan blue stained nuclei. An intact cell (bright white, trypan negative) is circled in red.