System checks for Illumina sequencing platforms

System checks are not required for normal operation and maintenance of an Illumina sequencing platform. However, an Illumina Technical Applications Scientist may ask you to perform a system check for troubleshooting purposes.

This bulletin outlines the system checks that can be performed and the time needed to complete the check for all Illumina sequencing instruments.

For all system checks, if an instrument wash is due, perform the wash before starting a system check. Always power cycle before performing the system checks.

iSeq 100

Time taken	Requirements	Procedure
45 minutes	Reusable test flow cell Reusable test cartridge	Remove reusable test flow cell and cartridge from storage. From control software menu, select System Check. (Mechanical, thermal, and optical sensor tests are selected) Unload to open compartment door and eject tray. Remove used cartridge from tray. Inspect the glass surface of the reusable flow cell for debris and clean with an alcohol wipe if needed. Dry with a low-lint tissue. Insert the reusable test flow cell into the reusable test cartridge with the label facing up. There should be an audible click. Place the reusable test cartridge onto the tray so that the access window faces up and the flow cell is inside the instrument. Select Load. Select Start to begin the system check. When the system check is complete, review whether each test has passed. If at least one test failed, contact Illumina Technical Support. Select Unload to eject the reusable test cartridge. Return the reusable test components to the original packaging and store at room temperature.

During the system check, the software ejects and retracts the cartridge one time, and displays the remaining number of uses onscreen. Both reusable components are valid for up to 130 uses. For more information, see the iSeq 100 System Guide.

MiniSeq

The appropriate system checks are preselected. Those that are unselected should only be performed by an Illumina engineer.

Time taken	Requirements	Procedure
20 mins	Used flow cell Wash cartridge	From the Manage Instrument screen, select System Check. When prompted to close the control software, select Yes. Add 40 ml deionized water to the wash cartridge in the reservoir equivalent to position 40 on the prefilled reagent cartridge. Load consumables as follows: If a used flow cell is not already on the instrument, load a flow cell. Empty the spent reagents bottle and return it to the instrument. Load the wash cartridge. Select Load. Select Next to start the system check. (Optional) When the system check is complete, select View next to the check name to view the values associated with each check. Select Next. The system check report opens. Select Save to save the report to a zipped file. When finished, select Exit. When prompted to close the service software and restart the control software, select Yes. Share the zipped results file with Illumina Technical Support.

For more information, see the MiniSeq System Guide

MiSeq

The Tip/Tilt and Full Optics tests require a special flow cell and should only be performed by an Illumina engineer.

Time taken	Requirements	Procedure
60 minutes	Used flow cell Wash tray Wash bottle	MCS v2.6 and older and MCS v3.1: From the Home screen, select Manage Instrument and then select System Check . MCS v4.0: From the Home screen, select the Hamburger menu in the top-left corner and then select System Check. Do one of the following: Select the individual tests that you would like to perform. Choose Select All to perform all tests If performing a volume test*: Fill each reservoir of the wash tray with 6 ml laboratory-grade water. Fill the 500 ml wash bottle with 350 ml laboratory-grade water. Load the wash tray and wash bottle onto the instrument. Make sure that a used flow cell is in place. Select Next. When complete, the test results appear on-screen. (Optional) Select Show Details to see a summary of the results. (Optional) Select Export Results to export the results in a *.csv file format. Select Done. Share the results with Illumina Technical Support.

\* If performing a volume test on a system running MCS 2.6 or lower only, you will need to raise and lower the sippers manually to check the PR2 position. When prompted remove any droplets from the wash bottle sipper, as follows:

1. Slowly raise the sipper handle and check the wash bottle sipper for the presence of a large water droplet.

2. Slowly lower the sipper handle far enough into the water to allow the surface tension to remove the droplet.

3. Slowly raise the sipper handle and check the wash bottle sipper for the presence of a large water droplet.

4. Slowly lower the sipper handle completely, making sure that the sippers lower into the wash bottle and waste bottle.

For more information see the MiSeq System Documentation

NextSeq 500/550

Time taken	Requirements	Procedure
90 mins	Used High Output flow cell Wash cartridge	From the Manage Instrument screen, select System Check. When prompted to closet the control software, select Yes. Load consumables as follows: If a used flow cell is not already on the instrument, load a flow cell. NOTE: Illumina recommends a high output flow cell for system check purposes. Empty the spent reagents bottle and return it to the instrument. Load the buffer wash cartridge containing 120 ml deionized water in the central reservoir. Load the wash cartridge. Make sure that the reagent wash cartridge is empty and clean. Select Load. Select Next to start the system check. (Optional) When the system check is complete, select View next to the check name to view the values associated with each check. Select Next. The system check report opens. Select Save to save the report to a zipped file. When finished, select Exit. When prompted to close the service software and restart the control software, select Yes. Share the zipped results file with Illumina Technical Support.

For more information, see the NextSeq 500 and NextSeq 550 Sequencing System Guide

NextSeq 1000/2000

Time taken	Requirements	Procedure
	None	From the control software menu, select System Checks. Select the checkbox for any of the system checks that you would like to perform. Select Start. Test results are output to the system-check folder located in /usr/local/illumina/systemcheck.

For more information, see the NextSeq 1000/2000 Product Documentation and the How To Perform a System Check on The NextSeq 1000/2000 video.

HiSeq 1000/2000/2500/3000/4000/X

The only system check on the HiSeq systems that can be performed by customers is the fluidics check.

Time taken	Requirements	Procedure
2-3 minutes per position	Used flow cell SBS bottles	Select Check on the welcome screen. Scan or enter the wash flow cell ID (barcode number) of the priming flow cell. Make sure to use a used flow cell for this step. Load the used flow cell onto the instrument. Fill eight SBS bottles with PW1 or laboratory-grade water, and load the bottles onto the SBS reagent rack. Select Solution 2 from the drop-down list. Confirm the following default values: Volume: 250 Aspirate rate (HiSeq 1000/2000/2500 high output mode): 250 Aspirate rate (HiSeq 2500 rapid run mode): 1500 Dispense rate: 2000 Select Pump. Inspect the flow cell for bubbles passing through the lanes, and leaks near the manifolds. If excessive bubbles are present: Check the manifold gaskets for obstructions. Reduce the aspirate rate to 100. Pump another 250 µl water to the flow cell.

For more information, see the appropriate System Guide: HiSeq 1000, HiSeq 2000, HiSeq 2500, HiSeq 3000, HiSeq 4000,

NovaSeq 6000

NovaSeq system checks should not be performed by customers unless asked by an Illumina scientist, and should be carried out under guidance. Power cycle the instrument before performing the system check

Time taken	Requirements	Procedure
1 hour to complete all tests	S3 wash flow cell OR S4 flow cell SBS wash cartridge and cluster wash tray for impedance test ONLY USED Buffer cartridge from previous run (wash buffer cartridge will not work)	Add 200 ml of water or BB3 wash buffer to position VB2 of the USED Buffer cartridge. After power cycling, close the NVCS and open the NovaSeq Service Software (NVSS) found on the desktop. Wait for NVSS to initialize. Load SBS Wash Cartridge, PE Wash cartridge, and USED Buffer Cartridge with 200 ml DI water onto instrument. Select Load flow cell from the home screen. Load S3 or S4 flow cell and select type from the descriptor drop-down menu. Starting a system check with the wrong flow cell type will give a ‘Wash flow cell is required’ error message Return Home Select System Check from Home Screen All tests are preselected Results will be pass/fail or NaN Select Start to run tests View Report option at end of system check will take you to the folder where the results were output Share the results folder with Technical Support.

For more information, watch the How To Perform A System Health Check On The NovaSeq 6000 video.

For any feedback or questions regarding this article (Illumina Knowledge Article #5873), contact Illumina Technical Support [e-mail].