Q system Flow Cell check (Q_FCC_revB_24Feb2023)
Protocol
V Q_FCC_revB_24Feb2023
FOR RESEARCH USE ONLY
Contents
Overview
Running the Flow Cell Check
1. Introduction to the Flow Cell Check
Purpose of the Flow Cell Check
A Flow Cell Check is used to assess the number of nanopores that are available in the flow cell. It should be done just before starting library preparation, and before the expiry date.
Oxford Nanopore Technologies will replace any flow cell that falls below the warranty number of 800 active pores, provided the result is reported within two days of performing the Flow Cell Check and the storage recommendations have been followed. If the number of active pores falls below warranty, please contact support@nanoporetech.com.
Flow cell storage instructions
We recommend storing flow cells unopened at 2-8°C. Check the expiry date on the flow cell pouch, and ensure you use the flow cell before the expiry date.
2. GridION flow cell check
Consumibles
- Celda de flujo MinION/GridION
Instrumental
- GridION
In this step, you will use the MinKNOW software to check the number of pores in your flow cell. This has to be done prior to loading your library onto the flow cell.
How it works
Flow cells are shipped with a QC DNA molecule present in the buffer. This molecule produces a distinctive nanopore signal. The MinKNOW™ software uses this signal to validate the integrity of the nanopore array before use and provides the user with an estimate of the number of simultaneously available channels for the experiment.
Connect the power cable to your mains/UPS solution. Use the mains cord supplied, or a suitable approved and rated power cord. Ensure the device is connected to a protective earth mains supply. Turn the power source on.
Press the power button. A blue light will appear in the middle of the button. The screen will show a loading page, followed by a login screen.
When the login screen appears, enter the password "grid" and log in.
Open the GridION lid and insert the flow cell.
Insert the flow cell in the GridION by sliding the flow cell under the clip. Firmly press down on the flow cell to ensure good thermal and electrical contact.
Click the Nanopore Wheel icon on the desktop to load the MinKNOW software. You will see the MinKNOW user interface appear.
We recommend users to log into the MinKNOW software using their Community credentials.
To log in, you must be connected to the internet.
From here, you can also change the language in the user interface in the bottom right corner.
You will be prompted to enter your email address and Nanopore password:
If you experience login issues, please visit the Community Support channel (https://community.nanoporetech.com/support) and use Continue as guest for temporary use.
Select the sequencing device.
The Sequencing Overview page should show the flow cell has not had any checks carried out.
Navigate to the start homepage and select 'Flow Cell Check'.
When you see the flow cell type and flow cell IDs recognised, click 'Start' to begin.
You will be automatically navigated to the Sequencing Overview page.
A loading bar appears under the flow cell during the checks.
This example is a Flongle CTC (loading bar highlighted in red). 
The flow cell check should take a few minutes.
Flow cell health indicators
The quality of the flow cell will be shown as one of the three outcomes on the Sequencing Overview page:
- Yellow exclamation mark: The number of sequencing pores is below warranty.
- Green tick: The number of sequencing pores is above warranty and ready for sequencing.
- Question mark: A flow cell check has not been run on the flow cell during this MinKNOW session.
Note: the indicator of quality will only remain visible during the MinKNOW session when testing occurred. Once the sequencing device has been re-started, the status of the flow cell will be erased.