Running a System Check on an iSeq 100

A system check on an iSeq 100 takes about 45 minutes and uses the reusable test flow cell and reusable test cartridge to troubleshoot pre-run check errors and other issues. Four subsystem tests confirm whether components are properly aligned and functional.

Normal operation and maintenance do not require a system check.

Use the following steps to perform a system check.

1. Retrieve the reusable test flow cell and reusable test cartridge from room temperature storage.

2. From the control software menu, select System Check.

   1. The System Check dialog box appears with the mechanical, thermal, optical, and sensor tests selected.

3. Select Unload to open cartridge compartment door and eject the tray.

4. If present, remove the used cartridge from the tray.

5. Inspect the glass surface of the reusable flow cell for visible debris. Under normal circumstances, the reusable test flow cell does not require cleaning. If debris is present, clean as follows.

   1. Clean the glass surface with an alcohol wipe.

   2. Dry with a low-lint lab tissue.

   3. Make sure that the flow cell is free of lint or fibers.

6. Hold the reusable test flow cell by the grip points with the label facing up.

7. Insert the reusable test flow cell into the slot on the front of the reusable test cartridge. An audible click indicates that the flow cell is in place. When properly loaded, the grip protrudes from the cartridge, and the glass is visible from the access window.

A. Loading the reusable test flow cell B. Loaded reusable test flow cell8. Place the reusable test cartridge onto the tray so that the access window faces up and the flow cell is inside the instrument.

1. Select Load to load the reusable test cartridge and close the door.

2. Select Start to begin the system check.

   1. During the system check, the software ejects and retracts the cartridge one time. The reusable test flow cell and cartridge are valid for 130 uses or 5 years from the date of manufacture. The remaining number of uses are displayed onscreen.

3. When the system check is complete, review whether each test passed or failed.

   1. If all four tests pass, the instrument is functioning properly, and the issue is likely consumable- or library-related. Set up a new run.

   2. If any of the four tests failed, this could indicate a hardware issue. Contact Illumina Technical Support at [e-mail] and provide the System Check results from D:\Illumina\iSeq System Checks\SystemCheckReport.[date/time].

      1. This folder can be attached to an email as it should be no larger than 3 Mb and even smaller when compressed/zipped.

4. Select Unload to eject the reusable test cartridge.

5. Remove the reusable test cartridge from the tray.

6. Remove the reusable test flow cell from the cartridge.

7. Return the reusable test components to the original packaging and store them at room temperature.

8. Close the System Check dialog box.

For any feedback or questions regarding this article (Illumina Knowledge Article #2298), contact Illumina Technical Support [e-mail].