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Instrument Cleaning Recommendations


To keep your Cytek Aurora or Northern Lights cytometer running smoothly, it's important to take good care of the fluidics system.  Below are Cytek's cleaning recommendations to maintain your system's fluidics.

Before the Start of Every Experiment  

  1. Load a new tube containing approximately 3 mL DI water. 
  2. Run water at high flow rate for 5 minutes. 

After Each Experiment

  1. In the “QC & Setup” or “Acquisition module”under the Cytometer tab, click on Clean Flow Cell and follow the instructions. You will need 10% bleach and DI water. Refer to this video tutorial for more details on keeping your flow cell clean.
  2. After completing Clean Flow Cell, leave the tube of DI water on the sample injection port (SIP) for the next user.    

    End of Day Fluidics Shutdown

    This procedure should be performed using the Tube delivery mode.  Refer to our video tutorial on Shutting Down the Cytometer for more details.

    1. If your system has a plate loader, ensure the gate shifter on the side of the loader is in the back position for Tube delivery mode. 
    2. In the “QC & Setup” or “Acquisition module”, under the Cytometer tab, click on Fluidics Shutdown and follow the instructions. You will need 10% bleach, DI water, and 30% Contrad 70.
    3. After completing Fluidics Shutdown, power off the system and close SpectroFlo as instructed in the pop-up window.   

    As Needed: Contrad Soak the Flow Cell

    Complete this procedure as needed; the frequency depends on how often the system is used, and what types of samples are going through the system.  If you notice increasing amounts of debris in your FSC vs SSC plot, and/or increasing FSC %rCV in the system's QC data, running this procedure will help clean out the flow cell. If you're not sure how frequently to contrad soak the flow cell, start with a monthly or weekly soak and increase frequency if needed.

    1. If your system is a shared system, reserve one hour for the next morning following the Contrad soak to wash out the Contrad from the system.
    2. Perform a Fluidics Shutdown using four tubes, each containing 3 mL 30% Contrad 70.
    3. After completing Fluidics Shutdown, unload the 30% Contrad tube and replace it with a fresh tube containing 3 ml of DI water.
    4. Power off the system and close SpectroFlo as instructed in the pop-up window and leave the system alone so the flow cell can soak overnight.
    5. The next morning, power on the system, open SpectroFlo, log in, wait for the software to connect to the cytometer, and perform a Clean Flow Cell using two tubes each containing 3mL DI water.
    6.  Load a new tube containing approximately 3mL of DI water onto the SIP and run it at high flow rate for 30 minutes.
    7. Perform QC and make sure it passes before running experiments.

              Monthly Long Clean 

              1. Prepare at least 1 L of 10% Bleach and two tubes, one containing 3 mL 10% bleach and one containing 3 mL DI water.
              2. Locate your Long Clean sheath bypass assembly and a new sheath filter, if needed.
                Note: We recommend replacing the sheath filter about once per year; if you have a Cytek service contract, the field service engineer will replace this for you during preventative maintenance visits.
              3. In the QC & Setup or Acquisition module, under the Cytometer tab, click on Long Clean and follow the instructions. For additional details, watch the video tutorial Performing a Long Clean.