How to Check if a MiSeq Cartridge was pierced during a run.

Users may encounter situations in which run quality is lower than expected. There are a variety of possible causes for low run quality. One potential cause is the reagent cartridge was incompletely pierced during the run. This results in failure of certain sequencing by synthesis (SBS) chemistry steps being unable to proceed due to lack of reagent flow. In order to determine if this was a factor in poor run quality:

1. Remove the cartridge from the MiSeq chiller. The sippers must be raised by either selecting "Start wash" or beginning the process of setting up a new run to access the previous cartridge.

2. Inspect the foil coverings on top of the cartridge at each position.

3. All wells should be pierced. If any well is not pierced, contact Illumina Technical Support to report the issue. Provide MiSeq serial number and the Reagent Cartridge Serial and Lot number (located on the box the cartridge was originally shipped in.)

For any feedback or questions regarding this article (Illumina Knowledge Article #3497), contact Illumina Technical Support [e-mail].