Best practices for preparing and inspecting NovaSeq 6000 flow cells for sequencing

Proper preparation and inspection of NovaSeq 6000 flow cells before sequencing reduces the occurrence of vacuum-related issues and helps to prevent instrument leaks. This article explains how to prepare and inspect NovaSeq 6000 flow cells for successful sequencing.
Best Practices for NovaSeq 6000 flow cell preparation and inspection
  1. 1.
    Remove new flow cell package from 2°C to 8°C storage.
  2. 2.
    Set the sealed flow cell package aside for 10–15 minutes to allow the flow cell to reach room temperature. Use the flow cell within 12 hours of removing it from the package.
  3. 3.
    Inspect the top and bottom surface of the flow cell for any damage, such as cracks or chips.
    1. 1.
      Contact Illumina Technical Support to evaluate the flow cell if chips are found on the bottom surface or cracks are found on either surface.
  4. 4.
    Inspect the flow cell for any particulate material within or nearby flow cell gaskets (see Fig. 1).
    1. 1.
      If particulate is observed, gently wipe away debris, or turn the flow cell over and gently tap the flow cell on the counter to remove the material.
    2. 2.
      If particulate obstructing the gasket cannot be removed, contact Illumina Technical Support to discuss whether to proceed with the use of the flow cell.
Figure 1. Example of material blocking the flow cell gasket.
  1. 5.
    Inspect the flow cell for cosmetic defects. Cosmetic defects can include variable iridescence across the flow cell, circular spots within the flow cell, scratches on the surface or within the flow cell, or chips on the top surface of the flow cell (see Fig. 2). Flow cells go through rigorous visual Quality Control (QC) before they are shipped. Cosmetic defects such as these rarely affect output or quality, and performance is guaranteed.
Figure 2. Variable iridescence across flow cell surface (left). Circular spots within the flow cell (middle). Flow cell scratches (right).
  1. 6.
    Before loading the flow cell on the NovaSeq 6000, inspect the flow cell and NovaSeq 6000 flow cell stage for glass shards and debris.
    1. 1.
      Glass shards can impact the vacuum seal needed for successful sequencing. For additional details, search for Knowledge Base article Troubleshooting NovaSeq 6000 flow cell loading issues Video.
    2. 2.
      Inspect the underside of the flow cell for any glass shards. If glass shards are present, use an alcohol wipe to clean the underside of the flow cell. Then dry the flow cell with a clean, dry, lint-free tissue.
    3. 3.
      Inspect the NovaSeq 6000 flow cell stage including the grooves, vacuum holes, and the manifolds.
      1. 1.
        If the flow cell stage appears free of debris or glass shards, use an alcohol wipe to clean the flow cell loading position, manifolds, and the flow cell clamp. Remove residual alcohol by wiping the flow cell stage with a clean, dry, lint-free tissue.
      2. 2.
        If debris or glass shards are observed (see Fig. 3), remove the debris by blotting the flow cell stage with an alcohol wipe. After blotting, visually inspect the flow cell stage to confirm that the debris has been removed. Remove any residual alcohol by wiping with a clean, dry, lint-free tissue.
Figure 3. Example of glass shards observed on the NovaSeq 6000 flow cell stage.
  1. 7.
    Contact Illumina Technical Support with any questions or concerns pertaining to the information outlined in this article. Technical Support can assess whether to proceed with flow cell use. Providing a picture of the flow cell and the lot/serial number information helps Illumina provide appropriate guidance.
For any feedback or questions regarding this article (Illumina Knowledge Article #1311), contact Illumina Technical Support [email protected]. For specific trademark information, please visit
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