How to perform a System Check on the MiSeq

System checks are not required for the normal operation and maintenance of an Illumina sequencing platform. Rather, the system checks are used for troubleshooting purposes.

• 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.

• System check results are located in the D:\DiagResults folder.

Instruction Steps:

* The Tip/Tilt and Full Optics tests require a special beaded flow cell and must only be performed by an Illumina Field Service Engineer (FSE).

** If performing a volume test on a system running MiSeq Control Software (MCS) 2.6 or earlier only, the sippers must be manually raised and lowered 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.

Additional Resources:

• MiSeq Control Software v4.0 or above: Page 39 of the MiSeq System Guide on Windows 10.

• MiSeq Control Software v3.1 or below: Page 42 of the MiSeq System Guide for Windows 7 and MiSeq System Guide for MiSeq Reporter.

• If any system check fails, consult this article Troubleshooting failed MiSeq system checks

For any feedback or questions regarding this article (Illumina Knowledge Article #1777), contact Illumina Technical Support [e-mail].