# Deep clean explained

## How to deep clean

See our [deep clean tutorial](/protocols/best-practices/deep-clean-1.md).

## When to deep clean

[Deep clean](/protocols/best-practices/deep-clean-1.md) your BactoBox® in these cases:

* **At least once a week.** Use the 15-minute option.
* To recover a flow cell that failed the QC test.\ <mark style="color:$info;">Try with the 15-minute option first. If the issue persists, try the 10-hour option.</mark>

See [Maintenance](/protocols/maintenance.md) for more information.

## Why deep clean is important

Your BactoBox® setup might contain hard-lived contaminants such as limescale or biofilm.

{% columns %}
{% column %}

<figure><img src="/files/uNbdfcHljeEfpfXN7fGY" alt=""><figcaption><p>Limescale as known from your tea kettle.</p></figcaption></figure>
{% endcolumn %}

{% column %}

<figure><img src="/files/fXm6apoUfa1rICMZq8Xd" alt=""><figcaption><p>Biofilm</p></figcaption></figure>
{% endcolumn %}
{% endcolumns %}

{% hint style="success" %}
Follow our guidelines (see [Maintenance](/protocols/maintenance.md)) to avoid build-up of hard-lived contaminants such as limescale and biofilm.
{% endhint %}

Especially the microfluidic flow paths inside the flow cell are sensitive to contaminants. The smallest cross-sectional area is 10×25 µm, which is approximately one-tenth the width of a human hair. Even relatively light contamination may influence the performance of the flow cell.

## What deep clean does

The *Deep clean* program scrubs your BactoBox® setup with our [deep clean vial](/encyclopedia/item-register/vials-flasks-and-liquids/deep-clean-vial.md). The deep clean vial contains a pepsin/HCl solution. In other industries, this solution is used to remove protein and limescale deposits from pH-electrodes made of glass. This solution also effectively cleans the flow cell in your BactoBox® setup.

The *Deep clean* program soaks the flow cell in the solution. It runs the pump intermittently to refresh the liquid in contact with the flow cell.


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