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How to Perform a System Check on the MiniSeq

The MiniSeq System Check process requires the following.

  • One wash flow cell (a previously used flow cell; this wash flow cell can be either a mid output or high output used flow cell. ).

  • One wash cartridge filled with 40 ml lab-grade water or 0.05% Tween in lab-grade water (loaded in well 40 as indicated below).

To perform the system check on the MiniSeq:

  1. Navigate to the Home screen in the MiniSeq Control Software (MnCS).

  2. Select Manage Instrument→System Check. a. MnCS automatically closes to allow the MiniSeq Service Software (MnSS) to launch.

  3. Perform the following steps (the instrument does not prompt this).

a. Load a wash flow cell (used flow cell).

b. Empty the spent reagent bottle and return it to the instrument.

c. Load a wash tray with 40 ml lab-grade water in the wash reservoir, position #40. (Note: The MnSS may present the prompt "Fill in BB3 with DI water prior the test. Re-insert reagent tray, then press OK". The BB3 position is the same as well position #40).

  1. The following tests are pre-selected (the unchecked tests are those performed by Illumina Engineers only).

Motion: FCLM & FAM, Stage Test Optics: Flow cell Registration Fluidics: Valve response, Pressure decay, Flow rate Thermal: Fans, Thermal probes

  1. Select Next to begin the system checks.

The system checks require manual input about 5-10 minutes after the check start during the pressure decay test.

The checks take approximately 20 minutes to run.

Once the test is complete, a read-out of each test showing Pass or Fail result appears on the screen.

  1. If all tests pass, the instrument is functioning properly, and any issue is likely consumable or library-related.

  2. If any of the tests fail, this can indicate a hardware issue. Contact Illumina Technical Support ([email protected]) and provide the System Check results from D:\Illumina\SystemCheckResults\SystemCheckResultsDetails.csv.

After reviewing the results, select Exit to close the MiniSeq Service Software and return to MiniSeq Control Software.

For any feedback or questions regarding this article (Illumina Knowledge Article #2040), contact Illumina Technical Support [email protected].

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