Cytometry and Antibody Technology

Getting started in the CAT Facility

Welcome to the CAT Facility. The information below will help you get started as quickly as possible. That said, the staff is always there to help you with any questions, problems, or requests you might have. We’ll be happy to support your project in any way that we can.


The CAT Facility offers a wide variety of services. All services can either be utilized by trained users without staff assistance (unassisted use) or samples can be dropped off to be run by our expert staff (assisted use). Trained users can access the CAT Facility 24/7 whereas staff assisted use of services is available during normal operating hours.

The best way to contact the staff is at – this will reach the entire CAT Facility staff. For immediate assistance during normal operating hours you can also call the lab at (773) 702-9212.

Please follow the New User Checklist below to get started! 


New to the Flow Cytometry Technology?

The CAT Facility staff works with users who have a range of experience levels. For those unfamiliar with the technology and/or the range of the services offered in our facility, a general overview can be found below.

  • Benchtop analyzers, ImageStream, Spectral analyzers: Analyze fluorescent antibodies/dyes/proteins bound to cells or particles. This will result in a data file that can generate plots and statistics, but you will not be able to recover your cells after running them through the flow cytometer.
  • All sorters: Analyze and sort cells or particles based on fluorescent antibodies/dyes/proteins. You will be able to select and isolate cells that can be utilized for downstream experiments (cell culture, sequencing, etc.). A data file will also be generated.
  • Multiplexing: Examine multiple analytes in a cell-free supernatant (i.e., cytokines in serum or tissue culture media)
  • Mass Cytometry: Analyze heavy metal-tagged antibodies on cells, useful for very high parameter panels or tissues with extreme autofluorescence.

We also have an FAQ page (located under the About menu) and Resources Library (located under the Resources menu) that has some useful information. Feel free to schedule a short meeting with the CAT Facility staff to discuss your project and determine which instrument will best suit your needs.

New User Checklist

  1. Sign up for our online scheduler (video tutorial here). Please provide your FAS or PO number in the iLab reservation window in the Payment Information box. The IRB number is also required if you are using patient samples, it can be entered in the Event Notes box. Click here to get a sense of where this boxes are. Note: the staff does not receive notifications from the iLab scheduler when instruments are scheduled by users. If you wish to use the services in a way that is different than the default assumption, please email or call the staff directly:
    • Benchtop analyzers, ImageStream, Spectral analyzers: all appointments are assumed to be run by trained users, contact the staff if you would like to request staff assistance for drop-off samples.
    • All sorters: all appointments are assumed to be run by staff during normal operating hours, contact the staff to discuss if training is appropriate.
    • Multiplex: most users discuss their multiplexing experiments with the staff prior to scheduling their first one.
    • Mass Cytometry, Antibody Services, Project Management, Drop-Off Samples: Contact the staff directly to schedule this service. Please see the Mass Cytometry and Staff Assistance pages for more information.
  2. Determine if you have access to the CAT facility. You may not need access to all locations.
    • Main Lab: The CAT Facility is located in a secured area of the BSLC building, room R022. For video instructions on how to get into the lab and a short lab tour, see the Contact Us page. The University of Chicago Hospital ID with proper authorization is needed to access this portion of the building. Contact the Technical Director if you do not have the required authorization.
    • The Satellite Facility in the Billings Hospital: One benchtop analyzer is located here. The UoC Hospital ID card is needed to circulate in the Billings Hospital, a key is needed to access room S301. The key is available upon request from the Technical Director.
    • PME Laboratory: The Helios Mass Cytometer and the PME instruments are located in the PME space. It is restricted to PME researchers.
  3. Schedule training relevant to the service you want to use.
Benchtop Analyzers

Staff-Assisted Use (Drop-off Samples)

If you wish to drop off samples for the staff to run no training is required. If you are new to flow cytometry you may find the Flow Basics Training Course useful, but you are not required to take it. Please check the Flow Basics page for more information about how to register for the zoom meeting, the upcoming course dates, and a PDF of the presentation.

For more information on the drop-off sample service, please check the Staff Assistance page for more information and procedures for scheduling.

Unassisted Use

All users who wish to use any analyzer (Fortessa, Attune, Quanteon, ImageStream, Aurora) unassisted are required to complete the Flow Basics Training Course. The hands on portion of the training is specific to the software that runs the equipment. Please note there is an additional course required to use the Cytek Aurora spectral analyzer (see the spectral training section for more information).

The hands-on training is charge for the amount of time used on the instrument at the regular rate.

For the Flow Basics Training course please check the Flow Basics training page for more information about how to register for the zoom meeting, the upcoming course dates, and a PDF of the presentation. Information regarding the hands-on portion can be found on the Instrument software training page.

For more information on our benchtop analyzers, see our benchtop analyzer page or the resources pages.

Spectral Analyzer (Cytek Aurora)

More information about spectral cytometry can be found on the Benchtop Analyzers page. Information specific to the Aurora can be found on the Aurora page.

After completing the mandatory benchtop analyzer training, you may request to be trained on the spectral analyzer. Training consists of a 2 hour course followed by 2 hour session for hands on training. We will provide samples for the hands-on training – you do not need to prepare anything. Please contact the staff for more information.

General training process is:

  1. Flow Basics Course (schedule on the Flow Basics page)
  2. Aurora Training Course (see YouTube playlist)
  3. Aurora hands on training
  4. Hands-on training for any other benchtop analyzers can be done at any time before you use another cytometer
Cell Sorters

Staff-Assisted Sorting

The cell sorting service is available to all users and the staff will normally operate the sorters on your behalf. The majority of our users choose this option. Please see our sorter page for more information, as well as the sorter section of the FAQ page (located under the About menu).

Unassisted Sorting

Currently, training for the cell sorters is limited to the FACSArias and the Tyto. Training for the Bigfoot is forthcoming.

Training for the FACSArias is offered to select users who plan on sorting heavily outside of normal operating hours and have experience with BD FACSDiva. If you have never used our facility previously you must complete the Flow Basics Course. Please contact the staff to determine if training is appropriate. The training regimen is very quick, so we expect the candidates to demonstrate proficiency with the flow cytometry technology and the operating software (BD FACSDiva).

The sorter training is in three sessions of two hours. The instructor will use the first session to illustrate the startup and shutdown protocols on the sorter, as well as the general workflow of setting up a sorting experiment. During the subsequent sessions, you will be initializing and operating the instrument under the staff supervision. It’s recommended to bring samples to sessions 2 and 3, but time actually spent sorting will be limited by the speed at which you can get the instrument ready, so we recommend a simple non-crucial experiment.

Please note that the unassisted cell sorting rate ($60/hr) only applies outside of normal operating hours (10AM-5PM). During normal hours, cell sorting is the same rate whether or not a staff member is operating the instrument ($90/hr). The cell sorter training is charged for the time booked on the instrument at the normal assisted rate.

Training for the Tyto, on the other hand, is provided at no charge. Typically, users will need staff assistance only to set up their initial sort template. Subsequent sorts using that template are easily performed without help from staff. However, you are welcome to request staff assistance if you wish to modify your template.


Training is not required for users wishing to utilize the Luminex 200 or Quickplex sq120 platforms. The staff will train you on these instruments without the need to go through the Flow Basics Training Course. Please contact the staff to discuss your project and how to get started.


Mass Cytometry, Antibody Services, Project Management, Drop-Off Samples: Contact the staff directly to schedule this service. Please see the Mass Cytometry and Staff Assistance pages for more information.

Not sure which service to get trained on first? The Flow Basics Training Course will provide you with a full overview of our services and many users start there. You can check the Flow Basics Training Course page for more information about how to register for the zoom meeting, the upcoming course dates, and a PDF of the presentation.

For all other questions please contact the staff.

  1. Read the facility use policies below.
  2. Determine if you have access to our data FTP server – logins are assigned by lab/PI. If not, please contact the CAT Facility staff to get one set up.
    • The data FTP server can be accessed using the link in the upper right menu at the very top of this website.
    • The data FTP server can also be accessed from any desktop FTP client. Instructions can be found here.
  3. Determine if you need a seat on our analysis software site license.
  4. Once you have completed the required training for the service of your choice, you may be interested in our optional training. Be sure to check the menu bar of our website to find our blog, resources, and additional training courses. We also offer consultation services where you can meet with our Scientific Associate Director to discuss your project – the first meeting is free.
  5. When you are ready to publish your data, be sure to check out our boilerplate texts for attribution, found under the “About” menu.
  6. External users: The CAT Facility welcomes users from outside the University of Chicago campus. External users will need to provide a purchasing order and generate an account on the iLab online scheduler. External rates may apply. Contact the CAT Facility to request a quote. Northwestern and the University of Illinois in Chicago are members of the Chicago Biomedical Consortium and as such are entitled to the internal rate.

CAT Facility Policies


We expect the users to let us know as soon as possible when an experiment needs to be cancelled. Cancellation requests must be submitted before the start of the reservation. Requests to cancel events past their start time will not be approved.

Cancelling a benchtop analyzer reservation: The iLab system allows for online cancellation up to 4 hours before the start of the reservation. Unused booked time will be charged in full.

Cancelling a sorting or mass cytometry experiment: Reservations on the FACSAria cell sorters can be cancelled by the user up until the point the iLab reservation has been marked as confirmed by the CAT Facility staff. Confirmed sorts and mass cytometry reservations must be cancelled 24 hours before the start of the experiment. Contact the CAT Facility staff to do so. Unused sorting or mass cytometry reservations will be charged in full.

Data Transfer and Management

The data generated on any of our instruments is transferred automatically to the OSRF server. Access to the server is available through the online portal. The use of storage device on the acquisition computers is not allowed.

To get access to the Portal, email the CAT Facility with your CNET ID, the full name of your PI, and the username you’ll wish to use.

It is the responsibility of each user to properly safeguard the data. The server and acquisition computers are not designed as safe storage space. Please take some time to make sure that you have collected every piece of data from our server. Contact the CAT Facility if you need assistance finding older data filesIf your lab does not have a storage solution, we recommend UChicago Box or CRI Research Data Storage.  As you may know, many peer-reviewed journals are now requiring that data be made available by request of an editor. Therefore it is becoming increasingly important for researchers to keep track of their raw data files. Online repositories such as FlowRepository can be used to store published data.

Data management Policy
– The data generated on any instrument will remain on the the acquisition computer for 1 month. Older data will be deleted.
– FCS files generated on any instrument in the facility are transferred automatically on the CAT Facility server. The use of external hard drive and USB sticks is not allowed on any instrument.
– Data files transferred to the server will remain for a period of three months. They are then backed up on a secondary server for an undefined period of time. Data on the secondary server may be deleted at any time with no advanced notice.
– The function of the CAT Facility server is to facilitate transfer of the data. We offer no guaranty for the safety of the data stored on it. Data preservation is ultimately the responsibility of the user.
Damage to Core Instrumentation

A university wide central shared research facility is one that is available to all faculty members and associated personnel on a first-come, first-served basis. In order to maintain state-of-the-art facilities on campus, it is necessary that all core facility users exhibit good citizenship and take care of our shared resources. Standard operating procedures specific to each core must be followed, including the completion of all required training necessary for use of each machine or technology. Additionally, users should adhere to any further directions given by core technical directors or staff.

Damage to an instrument or instrument malfunction must be reported to core staff immediately. Failure to do so may compound damage and expense. Minor damage may be covered by the core. Instruments require regular service and repair and these costs are built into the normal rates. However, PIs will be responsible for covering significant damage to equipment resulting from user negligence.

In the event of damage to an instrument that clearly resulted from a user’s failure to adhere to established operating protocols then the user’s principal investigator will be expected to pay for repairs not covered by service contracts. The technical director will notify the lab’s PI of the incident and charges.

Incidents may be reviewed by RROC including but not limited to financial implications.


The CAT Facility Can handle BSL1 samples, and BSL2 samples under specific conditions. 

If you will be using primary human samples or any other BSL2 material either on benchtop analyzers and cell sorters, visit the Biosafety page.