Procedures for cleaning flow cells for Illumina sequencers

iSeq 100

• No cleaning required.

• Only touch the plastic when handling the flow cell.

• Avoid touching the electrical interface, CMOS sensor, glass, and gaskets on either side of the glass.

• Reference: iSeq 100 Sequencing System Product Documentation.

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.

• Reference: MiniSeq System Guide.

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.

• Reference: MiSeq System Guide for Windows 10 and MiSeq System Guide for Windows 7.

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.

• Reference: NextSeq 500 and NextSeq 550 Sequencing System Guide

NextSeq 1000/2000

• The flow cell MUST NOT be cleaned.

• Flow cells can look streaky; they are fine to use.

• Reference NextSeq 1000/2000 Product Documentation.

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.

• Reference: NovaSeq 6000 Sequencing System Guide.

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.

• Reference: MiSeq i100 Plus System.

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