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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
HiSeq 2500
  • Remove the clustered flow cell from the container using a pair of plastistats.
  • Rinse the flow cell with laboratory-grade water. Dry with a lens cleaning tissue.
  • Fold an alcohol wipe to approximately the size of the flow cell.
  • Hold the edges of the flow cell with 2 fingers so that the inlet and outlet ports face up.
  • Wipe each side of the flow cell using a single sweeping motion. Repeat until clean, refolding the alcohol wipe with each pass.
  • Dry with a dry lens cleaning tissue.
  • Protect the flow cell from dust until ready to load it onto the instrument.
HiSeq 3000/4000/X
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.
For any feedback or questions regarding this article (Illumina Knowledge Article #5147), contact Illumina Technical Support [email protected].
Last modified 25d ago
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