> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001679.md).

# Best Practices for Washes on the MiSeq

**Background**

Many factors contribute to a successful sequencing run. One important maintenance practice is to ensure the system's fluidic lines are thoroughly washed between sequencing runs. It is also important that the fluidics systems are well maintained when the instrument is idle. This ensures that traces of old reagents are washed out so they cannot negatively impact sequencing performance.

This article outlines all different types of washes on the MiSeq and when they should be performed.

**Note:** When any wash is complete, leave the used flow cell, wash tray, and wash bottle containing the remaining wash solution in the instrument. The sippers remain in the down position, preventing the sippers from drying out and air from entering the system.

**Best Practices for Wash Solution**

Always make fresh wash solution for each wash. Use fresh Tween-20 and molecular-biology grade water. Older, dilute solutions of Tween-20 can encourage microbial growth and be detrimental to system performance.

**Wash Times**

* Post-Run wash: 20 minutes.
* Post-Run wash with Template line wash: 30 minutes.
* Maintenance wash: 90 minutes.
* Standby wash: 2 hours.

**Post-Run Wash:**

* Required after every sequencing run. At end of complete run, the MiSeq Control Software (MCS) will guide to set up the post-run wash.
* One step wash with 0.5% Tween 20 wash solution.
* 1. Add 6 ml wash solution to each reservoir of the wash tray.
  2. Add 350 ml wash solution to the 500 ml wash bottle.
  3. If the run showed no performance issues, you can use the old experimental flow cell to conduct the wash
* Expected wash waste volumes: 17.25 mls.

**Template Line Wash:**

* **Optional** for Research Use Only (RUO) runs. Can reduce trace sample carry-over contamination.
* Additional step to the regular post-run wash, with 0.5% Tween 20 wash solution.
* 1. Add 6 ml wash solution to each reservoir of the wash tray.
  2. Add 350 ml wash solution to the 500 ml wash bottle.
  3. Add 0.01% sodium hypochlorite (NaOCl, lab grade bleach) to the disposable wash tube in position 17 of the wash tray.\
     \* **NOTE**: It is important to make fresh NaOCl dilutions from stock.
* Expected wash waste volumes: 25.50 mls.

**Maintenance Wash**:

* Required every 30 days.
  * The instrument will display a warning notification that a maintenance wash is required 30 days from the last maintenance wash.
  * The instrument will prevent the user from starting a new sequencing run if a maintenance wash has not been completed within the previous 45 days.
* Involves **three** wash steps with 0.5% Tween 20 wash solution (prepared fresh for each wash step). MCS will guide on when to empty waste and refill the wash solutions for all three washes.
  1. Add 6 ml wash solution to each reservoir of the wash tray.
  2. Add 350 ml wash solution to the 500 ml wash bottle.
* Expected wash waste volumes: 51.75 ml.

**Standby Wash:**

* Prepares instrument for Standby mode.
  * Perform a standby wash if the instrument is unused for > 7 days and every 30 days thereafter if the instrument remains idle.
* Includes **two** wash steps with 0.5% Tween 20 wash solution (prepared fresh for each wash step). MCS will guide on when to empty waste and refill the wash solutions for both washes.

1. Add 6 ml wash solution to each reservoir of the wash tray.
2. Add 350 ml wash solution to the 500 ml wash bottle.

* When the Standby wash is complete, the instrument will be in **Standby** mode and a message appears on the home screen indicating the status of the instrument.
* To return the instrument to **Sequencing** mode, [power cycle](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001894) the instrument to reset system communications, then conduct a **Maintainance Wash** to bring the instrument out of standby mode.
* Expected wash waste volumes: 46.0 mls.

Additional information, please reference [MiSeq System Product Documentation](https://sapac.support.illumina.com/sequencing/sequencing_instruments/miseq/documentation.html).

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1679), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001679%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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