How do I clean my chips?

One simple but very effective way to clean a microchip is to flush an alkaline solution through the channels. A solution of 1 M sodium hydroxide in water works well, but a lower concentration might also be sufficient. If traces of the cleaning solution remain inside the chip after cleaning, rinse with water or ammonia. Note that caustic solutions can cause damage to e.g. the polyimide coating of fused silica capillaries. Further, plastic parts should not be exposed to alkaline solutions.

To remove particulate matter from your chip, a water bath with ultrasonic agitation can be used, preferably while flushing a watery solution through the channels using a Fluidic connection kit.

Glass microchips can be heated (e.g. >400° C) causing any organic material on the glass surface to degrade. Try to use lower temperatures first because burning the content could make it stick. Make sure you only heat the glass chip and not the plastic parts around it.

Concentrated sulfuric acid works well to dissolve organic material, such as fibres, that are difficult to remove with alkaline solutions. Always keep in mind that you are working with extremely corrosive material.

Please note that chips that were coated by Micronit have different guidelines for cleaning!

How do I clean my resealable flow cell's / OOC top and bottom layers?


Resealable flowcells are produced in cleanroom facilities and clean areas to prevent physical impurities. After use, cleaning might be required to remove organic residues. Please use distinguished cleaning processes for glass slides with and without a gasket.

Glass slides with gasket:

  • Can be cleaned with ethanol, isopropanol and acetone. The glass slides could be either immersed in the solvents or rinsed with them. Immersion might lead to diffusion of solvents into the gasket. Therefore, it is recommended to rinse the glass slide with the gasket thoroughly with water or buffer to remove residues.
  • Only wipe with lint free tissue, otherwise the sealing might be affected negatively or completely lost.
  • It is advised to not wipe the gasket as this might damage it and reduce its sealing abilities.
  • Physical cleaning of the surface by either heat (with a maximum temperature of 140 °C) or oxygen plasma is possible.
  • Cleaning with acids or bases has not been fully tested.

Glass slides without gasket:

  • Can be cleaned with organic solvents.
  • Can be gently wiped with tissue.
  • Physical cleaning of the surface by either heat up to 400 °C or oxygen plasma treatment is possible.
  • Alkaline solution can be used to clean the surface, e.g. 1 M sodium hydroxide in water.
  • Concentrated sulfuric acids could dissolve organic material, but are extremely corrosive, therefore it is not advised to use those. Hydrochloric acid could be used for cleaning, as well as bleach.

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