How to perform a NextSeq 500/550 system check

Note: For the system checks run via NextSeq Control Software (NCS) 4.0, the NextSeq Service Software (NSS) requires Local Run Manager (LRM) credentials.

How to run a system check in NCS:

1. Navigate to the Home screen in NextSeq Control Software (NCS).

2. Select Manage Instrument > System Check, then select yes to service software opening.

3. Load the following: a. A used high output flow cell (a high output flow cell is recommended, as mid output flow cells can lead to false flow rate failures). b. An empty the spent reagents tray. c. A buffer wash tray with 150 ml of lab-grade water in the center reservoir. d. An empty reagent wash tray.

4. The tests will be pre-selected (do not select unchecked tests, as the unchecked tests can only be performed by Illumina personnel).

5. Start the check (will take ~90 mins).

6. The results of the tests are saved to D:\Illumina\SystemCheckResults[Test]\Date; a screenshot of the results summary screen is also helpful to Illumina Support. Passing system checks are indicated with green checkmarks and a PASS record for the test.

Note: The new NextSeq 550 buffer wash cartridge has a label listing the minimum (150 ml) and maximum allowable volumes. 120 ml, as listed in the NextSeq 550 system guide, can alternatively be used.

For any feedback or questions regarding this article (Illumina Knowledge Article #1883), contact Illumina Technical Support [e-mail].