Cytometry and Antibody Technology

The CAT Facility can handle BSL1 samples on all instruments and BSL2 samples with specific instruments (described below). BSL2 samples should be fixed whenever possible. BSL3 samples are not allowed in the Facility.

Responsibilities for Biohazardous Samples: All users are responsible for obtaining the proper approval and training regarding biosafety before use of the instrumentation in the CAT facility. All users working with unfixed microorganisms that can be hazardous to humans, plants, or animals, or unfixed human cells (primary cells or cell lines), or other potentially biohazardous agents:

  • Are expected to have completed ORS training programs as appropriate. Read and understand the Agent Profile Form for your pathogen(s)
  • Must fill out the CAT Facility Biosafety Questionnaire at the bottom of this page prior to use of the instrumentation in the facility. The form should be submitted for each new biohazardous agent.
Instrument Usage
  • Follow the Procedures for Unfixed Biohazardous Samples described below
  • For the cell sorting service, not all sorters can run biohazardous samples. If a sorter not designated for biohazardous samples is scheduled the staff will not run the samples and the appointment will be rescheduled on an appropriate sorter.
Facility Usage
  • No eating, drinking or applying cosmetics in the CAT Facility
  • Any trash that comes into contact with biohazardous materials (such as sample tubes or plates) must be discarded in a designated biohazard bin


Procedures for Unfixed Biohazardous Samples

  1. Decontamination of Sample Tubes:
    • The sample should be disinfected with the disinfecting agent listed in your lab’s IBC protocol and Agent Profile Form prior to leaving your lab. Upon entering the CAT Facility, decontaminate the outside of your sample again with 70% ethanol.
  2. Running biohazardous samples
    • Samples must remain capped while vortexing
    • Post a sign at the cytometer indicating a biohazardous agent is being used while working. Consult the Office of Research Safety for guidance.
    • Samples CANNOT be manipulated in the Facility. This means any pipetting, filtering, etc. must be done in your own lab.
    • Do not use any sample retrieval options as it may lead to spills.
  3. Decontamination of cytometer and work surfaces:
    1. Run a tube of 10% bleach for 2 minutes on high, followed by a tube of water for 2 minutes on high.
    2. Wipe down the front of the cytometer, workstation (keyboard and mouse), and other work areas with 70% ethanol. If the agent you are working with is resistant to ethanol, use another appropriate agent followed with 70% ethanol wipe down. Consult the Office of Research Safety for guidance.
  4. Spill control:
    • Users must bring a spill kit and are responsible for cleaning up spills – typically freshly prepared 10% bleach and paper towels. Consult the Office of Research Safety for guidance (call 773-834-2707).
    • Contact the staff if a spill occurs inside the instrument.


Available Instruments

Biohazardous samples can be run on the instruments listed below. Please contact the staff if you have any questions. 

Attune NxT

Traditional Analyzer

Quanteon and Penteon

Traditional Analyzers


Spectral Analyzers
Aurora Blue, Aurora Red

Image Stream MarkII

Imaging Flow Cytometer


Droplet-Based Sorter
Traditional and spectral capabilities


Droplet-Based Sorters
FACSAria Fusion ONLY

MACSQuant Tyto

Mechanical Sorter

CAT Facility Biosafety Questionnaire

Please fill out the form below prior to using the CAT Facility instruments. Existing users must fill out the form for any new agents.

Biohazardous Samples


BSL2 Specimen Information

Please specify sample species:
Has the sample been screened for blood borne pathogens?
If the cells are from culture, are they transduced with a viral vector?
Does the sample contain any other known human or animal infectious agent(s), viral vectors or recombinant DNA materials?


If appropriate please state your IBC, IACUC, and/or IRB protocol number(s).

Instrument Usage

Select the instruments being used for this project
Type your name in the box below to acknowledge that you have read the CAT Facility Biosafety Policy at the top of this page and agree to follow the procedures described in this policy.

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