Washing the NovaSeq 6000

There are two types of washes on NovaSeq 6000.

• Automatic post-run wash

• Manual Maintenance wash

Automatic post-run wash:

• Performed automatically after every sequencing run.

• The software automatically initiates an automatic post-run wash using the wash solution and NaOCl provided in the reagent cartridge.

• Approximate time: 80 minutes.

Manual Maintenance wash:

• A maintenance wash is required when:

  • There has not been a 4-lane run with a post-run wash within the last 14 days.

  • There has not been a maintenance wash within the last 14 days.

  • A post-run wash fails prematurely or is incomplete.

• Approximate time: 80 minutes.

Note: NovaSeq Control Software (NVCS) v1.4+ will have staggered start countdown timer, which also applies to being able to perform a wash. The NVCS staggered start time indicates the instrument's availability for starting a new run or a wash. A maintenance wash for a single side can only be started when the other side is either idle or performing SBS (sequencing chemistry) read cycles. For more information, refer to Staggered Start of Runs in the NovaSeq 6000 Sequencing System Guide.

Required Reagents and Consumables for Maintenance Wash:

1. 0.05% Tween 20 wash solution:

• To a 500 ml centrifuge bottle, add 0.2 ml 100% Tween 20 to 400 ml laboratory grade water.

• Invert to mix.

• Add wash/tween solution to the center well of the SBS wash cartridge. Fill to the fill line, which indicates the minimum required volume.

• The other reservoirs remain empty.

2. 0.25% NaOCl:

• To a 30 ml centrifuge tube, combine 1 ml 5% NaOCl and 19 ml deionized water.

• Load 5 ml of the prepared solution into position 17 of the cluster wash cartridge.

  

3. 4-lane wash flow cell.

4. SBS wash cartridge.

5. Cluster wash cartridge.

6. Leave the used buffer cartridge from the previous run in place.

Note: A used buffer cartridge is required for maintenance washes to collect the wash liquid used to wash the lines. The buffer cartridge should be emptied or changed regularly. If a used buffer cartridge is not available, contact Illumina Technical Support to bypass the buffer RFID check.

Steps to Start a Wash:

1. Load the Wash Flow Cell.

2. Load the Wash SBS and cluster cartridges.

3. Empty Used Reagent Bottles.

• Note: This step is extremely important because the small bottle collects used reagents even if the system is configured to route used reagents externally.

4. Start the wash.

For more detailed instructions on how to perform system check, refer to NovaSeq 6000 system guide (pages 50-54).

Note: After the wash is completed, leave the consumables/cartridges in place until the next run.

Maintenance recommendations for wash cartridges:

• Clean and invert wash cartridge when not in use to prevent microbial growth/contamination.

• The lid for the wash cartridge (well 40) can bend sippers if not positioned correctly. A run can be started without the lid, as it is just a splash guard.

Maintenance recommendations for Wash Flow Cell:

• The wash flow cell is also known as S3 Wash Flow Cell

• The lifespan of a wash flow cell depends on the gaskets for proper sealing of the vacuum. Each wash flow cell typically lasts for approximately 100 washes.

• A wash flow cell with worn-out gaskets will fail the RFID registration of the wash flow cell, and cannot be used.

For any feedback or questions regarding this article (Illumina Knowledge Article #2484), contact Illumina Technical Support [e-mail].