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How to proceed if my flow cell has a bubble?

It is best practice to avoid introducing air into the system for optimal flow cell performance. Please refer to the following lesson video for a demonstration of flow cell priming and loading, as well as some additional tips and tricks.

Depending on the type of bubbles please follow the recommendations below:

1. How to avoid introducing bubbles during priming and loading: To avoid introducing bubbles at this step, you should make sure that you have no air at the end of the pipette tip before loading. If a small amount of air is visible in the tip, please hold the pipette man as vertically as possible and dial the volume setting down to bring the liquid to the tip. Leave a few microliters of fluid in the tip behind while loading to avoid introducing air.

2. Bubbles present in the inlet channel: These bubbles will not be visible on an intact flow cell, but can be removed by re-drawing about 15 - 20 uL of buffer from the flow cell (via the priming port). There is enough buffer in the outlet channel so that even if you remove about 15 uL you will still have the flow cell covered at all times with liquid.

Monitor the sensor array while dialing up to ensure that the pores stay covered in buffer. If bubbles in the inlet channels are positioned in a corner and do not move by withdrawing liquid, it is best practice to leave them there and be careful while loading the flow cells so that the bubble does not get dislodged.

3. Bubbles present under the priming port: To prevent bubbles while priming or loading, please ensure that you remove any air immediately beneath the priming port by inserting a P1000 tip and dialing up on the volume setting until you see approximately 10 uL of buffer enter the tip.

4. Small bubbles, either in the inlet channels or in the pore area, present before using the flow cell and also building during a run are not a concern and the flow cell should be used as normal unless the platform QC indicates otherwise.

5. Bubbles in the waste channel: bubbles produced in the waste channel during a run in normal and will not have an impact on the pores or run.

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