Flow Cell Check (PQE_1004_v1_revAL_25Apr2025)
Protocol
Flow Cell Check V PQE_1004_v1_revAL_25Apr2025
For Research Use Only
FOR RESEARCH USE ONLY
Contents
Overview
Running the flow cell check
Overview
For Research Use Only
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 run when you are ready to use the flow cell, and within 12 weeks of purchase of the MinION™ and PromethION™ Flow Cells (except for Flongle™ Flow Cells, which have a 4 week warranty). Flow cells in 'Early Access' phase have a 4 week warranty.
Oxford Nanopore will replace any unused flow cell that falls below the warranty number of active pores, provided the result is reported within two days of performing the flow cell check and the recommended storage conditions have been followed, as indicated in the Table below.
| Flow cell | Warranty number of active pores | Storage conditions for unopened flow cells |
|---|---|---|
| Flongle™ | 50 | +2°C to +8°C for 4 weeks |
| MinION™/GridION™ | 800 | +2°C to +8°C for 12 weeks |
| PromethION™ | 5000 | +2°C to +8°C for 12 weeks |
Use the flow cell check in the MinKNOW™ software to check the number of pores in your flow cell.
Download and install the latest MinKNOW version for your device.
Instructions can be found in the MinKNOW protocol.
How the flow cell check works:
Flow cells are shipped with a QC DNA molecule present in the storage buffer. The MinKNOW software uses this QC molecule to provide an estimate of the number of active pores available on the flow cell.
2. MinION and Flongle Flow Cell check
Make sure your MinION is connected to a computer and is plugged in and powered on or your GridION is plugged in and powered on.
Flow cell insertion into sequencing device:
MinION Flow Cell insertion
Open the MinION or GridION device lid and insert the MinION Flow Cell by sliding it under the clip. Firmly press down on the flow cell priming port cover (situated in the middle of the flow cell) to ensure good thermal and electrical contact between the flow cell and the device.
Flongle Flow Cell insertion
- Open the MinION or GridION device lid and insert the Flongle adapter by sliding it under the clip. The adapter should sit evenly and flat in the MinION or GridION device.
Note: The device should be plugged in and powered on before you insert the Flongle Flow Cell into the adapter.
- Slide the Flongle Flow Cell into the adapter and press the flow cell down until you hear a click. The flow cell should sit flat inside the adapter.
Close the device lid.
When a flow cell is inserted into the MinION Mk1D, the device lid will sit on top of the flow cell, leaving a small gap around the sides. This is normal and has no impact on the performance of the device.
Double-click the MinKNOW icon to open the MinKNOW UI.
Note: If you experience login issues, please visit the Community Support channel for assistance and use Continue as guest temporarily.
Navigate to the Start page and select 'Flow cell check' to open the flow cell check page.
Check the 'Flow cell type' and 'Flow cell ID' have been recognised. If not, add the information required. Click 'Start' to begin.
Note: For the Flongle Flow Cell, make sure to fill in the 'Flow cell ID'.
For Flongle, the 'Flow cell ID' is not automatically assigned in MinKNOW. It is imperative the 'Flow cell ID' is entered in the correct format: ABC123 i.e. ([A-Z] x 3 [0-9] x 3).
The ID is case sensitive with no spaces. The MinKNOW software will not allow you to proceed until the 'Flow cell ID' has been entered correctly.
The Flongle Flow Cell ID is shown in the blue box below:
You will be automatically navigated to the Sequencing Overview page.
A loading bar will be displayed under the flow cell during the check.
The flow cell check should take a few minutes.
Flow cell warranty
The indicator should show one of three statuses:
Yellow exclamation mark (Flongle Flow Cell): The number of sequencing pores is below warranty. Take the flow cell out of the device, re-insert it and run a flow cell check again. Refer to the FAQs for flow cells if required. If the flow cell is still below warranty, email support@nanoporetech.com or contact our Customer and Technical Services teams using the contact support function.
Green tick (MinION Flow Cell): The number of sequencing pores is above warranty.
Orange question mark (Flongle Flow Cell): 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 a MinKNOW session. Once the MinKNOW session has ended, the status of the flow cell will be erased.
3. PromethION Flow Cell check
After taking the flow cells out of the fridge, wait 20 minutes for the flow cells to reach room temperature before inserting into the PromethION. Condensation can form on the flow cell in humid environments. Inspect the gold connector pins on the top and underside of the flow cell for condensation and carefully wipe off with a lint-free wipe if any is observed. Ensure the heat pad (black pad) is present on the underside of the flow cell.
Make sure your PromethION device is plugged in and powered on.
Flow cell insertion into the sequencing device:
Flow Cell insertion into the PromethION P24/48
- Load the flow cells to be run into the docking ports of the PromethION 24/48.
- Insert the connector fully into the docking port and press down on the flow cell. Make sure that the flow cell is latched down completely.
Correct insertion of PromethION Flow Cells into a PromethION 24/48 device
Line up the flow cell with the connector (horizontally and vertically) and smoothly insert it into position.
Press the flow cell down firmly into the loader, and ensure that the latch engages.
Insertion of the flow cell at the wrong angle can damage the pins on the PromethION and affect your sequencing results. If you find the pins on a PromethION position are damaged, please contact support@nanoporetech.com for assistance.
Flow cell insertion into the PromethION 2 Solo and PromethION 2 integrated
- Place the flow cell flat on the metal plate.
Note: Make sure that the dark grey heat pad on the underside of the flow cell is not torn or deformed.
Slide the flow cell into the docking port until the gold pins cannot be seen.
Press the flow cell firmly into the loader until a click is heard.
Close the device lid.
Double-click the MinKNOW icon to open the MinKNOW UI.
Note: If you experience login issues, please visit the Community Support channel for assistance and use Continue as guest temporarily.
Navigate to the start homepage and click 'Flow cell check'.
Select the flow cells to be checked. When you see the flow cell type and flow cell IDs recognised, click 'Start' to begin, otherwise enter the information required.
You will be automatically navigated to the Sequencing Overview page.
A loading bar will appear under the flow cell during the check.
The flow cell check should take a few minutes.
Flow cell warranty
The indicator should show one of three statuses:
Yellow exclamation mark: The number of sequencing pores is below warranty. Take the flow cell out of the device, re-insert it and run a flow cell check again. Refer to the FAQs for flow cells if required. If the flow cell is still below warranty, email support@nanoporetech.com or contact our Customer and Technical Services teams using the contact support function.
Green tick: The number of sequencing pores is above warranty.
Orange 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 a MinKNOW session. Once the MinKNOW session has ended, the status of the flow cell will be erased.