Comment on page

Troubleshooting SIPDOWN Errors on the MiSeq

The MiSeq Control Software (MCS) will show a SIPDOWN error if the reagent sippers are not functioning or cannot lower to pierce the foil on the reagent cartridge.* This can be caused by physical obstruction (if the reagent cartridge is not fully inserted or is damaged), a hardware problem with the sipper assembly, or a communication error.
  • When present, this error occurs before the run starts, when the sippers first lower, immediately after selecting the start button.
  • This error can present in older versions of MCS as an Object Reference error.
**Troubleshooting steps:**1. Verify the reagent cartridge is fully inserted all the way to the back of the instrument chiller compartment.
  • Remove the reagent cartridge and verify no damage to the exterior of the cartridge. Confirm the reagents are fully thawed*.
  • Confirm if reagents foils are pierced.
  • Store the reagent cartridge, PR2 buffer, and the current flow cell in the buffer in the fridge (4°C).
  1. 2.
    Power cycle* instrument to reset communications.
  2. 3.
    After MCS re-initialization, select post-run wash.
  3. 4.
    Perform the post-run wash with a previously used flow cell and the MiSeq wash cartridge.
  • Often, the run can be re-started with the same consumables. However, if those consumables are used to complete the post run wash prior to reloading, the run will fail.
  • The post-run wash MUST be completed with previously used consumables and/or wash specific consumables.
  1. 5.
    If there is no indication of damage to the reagent cartridge, and the post-run wash completes successfully, restart the run with the same consumables.
  2. 6.
    If the reagent cartridge looks damaged, contact Illumina Technical Support and provide the reagent serial number (SN), cartridge lot number, and cartridge expiration date.
For further information, search for the following Knowledge Base articles:* Troubleshooting Sipdown Errors on the MiSeq Video.
  • *Reagent Stability and Thawing Guidelines for MiSeq Sequencing Kits
  • *How to Shut down or power cycle the MiSeq.
  • *How to Power Cycle the MiSeq Video.
  • Wash best practices for MiSeq.
For any feedback or questions regarding this article (Illumina Knowledge Article #1456), contact Illumina Technical Support [email protected].
© 2023 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners. Trademark information: Privacy policy: