Procedures for cleaning flow cells for Illumina sequencers

iSeq 100

MiniSeq

  • Put on a new pair of powder-free gloves.

  • Remove the flow cell from the container.

  • Clean the glass surface of the flow cell with a lint-free alcohol wipe.

  • Dry with a lint-free lens cleaning tissue. Use care around the black flow cell gasket.

  • Inspect the flow cell port for obstructions. Make sure that the gasket is well-seated.

MiSeq

  • Put on a new pair of powder-free gloves.

  • Remove the flow cell from the container.

  • Lightly rinse the flow cell with laboratory grade water until both the glass and the plastic cartridge are thoroughly rinsed of excess salts.

  • Using care around the black flow cell port gasket, thoroughly dry the flow cell glass and plastic with a lint-free lens cleaning tissue. Gently pat dry in the area of the gasket and adjacent glass.

  • Clean the flow cell glass with an alcohol wipe. Make sure that the glass is free of streaks, fingerprints, and lint or tissue fibres.

  • DO NOT USE THE ALCOHOL WIPE ON THE FLOW CELL PORT GASKET.

  • Dry excess alcohol with a lint-free lens cleaning tissue.

  • Inspect the flow cell port for obstructions. Make sure that the gasket is well-seated. If the gasket appears to be dislodged, gently press it back until it sits securely around the flow cell ports.

NextSeq 500/550

  • Remove the flow cell from the foil packaging.

  • Open the clear plastic clamshell package and remove the flow cell.

  • Clean the glass surface of the flow cell with a lint-free alcohol wipe. Dry the glass with a low-lint lab tissue.

NextSeq 1000/2000

NovaSeq 6000

  • It is not necessary to clean the flow cell.

  • If desired, clean the glass surface of the flow cell with a lint-free alcohol wipe. Dry the glass with a low-lint lab tissue.

NovaSeq X Series

  • Put on a new pair of powder-free gloves to avoid contaminating the glass surface of the flow cell.

  • With the flow cell foil package over a flat surface, peel open the foil from the corner tab

  • Remove the flow cell from the package. Grasp the flow cell by the sides to avoid touching the glass or the underside gaskets.

  • Always clean the flow cell, whether or not a contaminant is present, using the following steps:

    1. Wet a Contec Polynit Heatseal wipe with isopropyl alcohol (70%).

    2. Gently clean the applicable surface. Wipe in a lengthwise direction (top to bottom direction) only, avoiding gaskets and manifolds.

    3. Repeat steps a and b until surfaces are clear.

    4. Dry with a new polynit heatseal wipe or an unused side of the used wipe to avoid contamination.

  • Do NOT use other lint-free wipes such as Kim Wipes or similar products. Only use Contec Polynit Heatseal wipes.

  • Always use isopropyl alcohol over ethanol due to higher purity.

  • Reference: NovaSeq X Series.

MiSeq i100

  • No cleaning required (CMOS patterned flow cell integrated into the Dry cartridge).

  • Cartridge should be gripped from the side to avoid touching the flowcell circuit/CMOS sensor.

For any feedback or questions regarding this article (Illumina Knowledge Article #5147), contact Illumina Technical Support [email protected].

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