# 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](https://support.illumina.com/downloads/iseq-100-system-guide.html).
**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](https://support.illumina.com/downloads/miniseq-system-guide-1000000002695.html).
**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](https://support.illumina.com/downloads/miseq_system_user_guide_15027617.html) and [MiSeq System Guide for Windows 7](https://support.illumina.com/downloads/miseq_system_user_guide_win7.html).
**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](https://support.illumina.com/downloads/nextseq-500-550-systems-product-documentation.html)
**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](https://support.illumina.com/downloads/nextseq-1000-2000-product-documentation-200027171.html).
**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](https://support.illumina.com/downloads/novaseq-6000-system-guide-1000000019358.html).
**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](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/FrontPages/NovaSeqX.htm).
**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](https://support-docs.illumina.com/IN/MiSeqi100Series/Content/IN/FrontPages/MiSeqi100.htm).
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #5147), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005147%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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