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.


All new users should sign up for our scheduler and mailing lists. (Note: if you sign up for the Flow Basics Course, you will automatically be added to the mailing list. You do not need to fill out the mailing list form as well) A video explaining how to use the iLab scheduler can be found here. While we provide training on most of our platforms so that users can run experiments independently, we also provide the assisted-use service on all platforms where an expert member of the staff will process the samples on the instruments. In general, most users prefer to be trained on the benchtop analyzers, while cell sorting is mostly an assisted-use service. Mandatory training is required for unassisted benchtop analysis. Additional training is required for unassisted cell sorting and for Spectral Flow Cytometry.

Mandatory training on benchtop analyzers

UPDATE FOR COVID: Training has moved online, please Check the Training Courses page for more information about how to register for the zoom meeting. Hands-on training is also completed using zoom so that social distancing is maintained. The hands-on session is now broken into two one hour sessions.

A mandatory 2-hour training is offered to provide you access to the instruments in the facility. The training is in two parts: one is a 1hr course called Flow Basics where we go over the fundamentals of the instrument and provide some pointers about how the data should look like. The course is presented every other Wednesday in room R023 of the BSLC building at 10AM. Check the Training Courses page for the next availability and a .pdf of the presentation. Bring your own copy of the presentation if you wish, we will not provide handouts at the training – no registration needed, just drop in. The second part is a hands-on 1hr one-on-one training session on one of our instruments. While it is not absolutely essential, we prefer that users bring samples so we can demonstrate how the instrument works. The Benchtop analyzer training is free.

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

Cell sorter training

UPDATE FOR COVID: Please check the homepage for the link to the detailed procedures for the current phase. Samples should be dropped off so that social distancing can be maintained. For training, please contact the staff – we can accommodate training with the use of zoom.

The cell sorting service is available to all users and the staff will normally operate the sorters on your behalf. Please see our sorter page for more information, including the sample preparation guide and FAQ.

The cell sorter training is offered to users who plan on sorting heavily outside of normal operating hours. The training regimen is very quick, so we expect the candidates to demonstrate proficiency with the flow cytometry technology and the FACSDIVA software.

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 Aria, as well as the specificities of setting up a sorting experiment on the Aria. During the other two sessions, you will be setting up the instrument under the staff supervision. If you wish, you can bring samples to sort during sessions 2 and 3. The sorting time 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 charge ($60/hr) only applies outside of normal operating hours (10AM-5PM). During normal hours, cell sorting is the same price wether or not a staff member is operating the instrument ($90/hr). The cell sorter training is charged $350/user.

Spectral Analyzer (Cytek Aurora) training

After completing the mandatory benchtop analyzer training, you may request to be trained on the spectral analyzer. Training consists of a 1.5 hour course followed by 1 hour of hands on training. We will provide samples for the hands-on training – you do not need to prepare anything. Please contact Laura Johnston for more information.

Scheduling time on the instruments

The CAT Facility uses the iLab LIMS for instrument scheduling and billing. You will need to create your own account here.

Booking time on any instrument is done through the Schedule Equipment tab.

  • When booking a bench top analyzers, it is assumed that you will not require the assistance of a member of the staff. If you do need help, let us know.
  • When booking time on a cell sorter or the mass cytometer, it is assumed that you will require assistance to run the instrument. A few days before your experiment, a staff member will review and confirm your reservation in iLab to ensure there is no panel design issues. The staff will be present at the time of your experiment to operate the sorter.

You can contact the staff directly to get assistance on an instrument other then a sorter or mass Cytometer, or if you need a specialized service. These requests would include:

  • The drop-off service, where you leave a member of the staff with your stained samples to have them run on any instrument
  • The project Management service, where you get assisted by the Associate Scientific Director with your experiment.
  • The monoclonal services (antibody purchase, antibody conjugation, etc)

More details on these services can be found 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.

Cancellation Policy

We expect the users to let us know as soon as possible when an experiment needs to be cancelled. Cancellation requests must be presented before the start of the reservation. Request for past reservation will not be processed.

Cancelling a bench top 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 at 80% of the value of the reservation.

Cancelling a sorting or mass cytometry experiment: Reservations on the Aria 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 Policy

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 is not allowed.

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.
– Data 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 there for one year after the date of creation. Older data will be deleted.
– The function of the CAT Facility server is to facilitate transfer of the data. Data preservation is ultimately the responsibility of the user.
CAT Facility access

Main Lab
The CAT Facility is located in a secured area of the BSLC building. The University of Chicago Hospital ID with proper authorization is needed to access the portion of the building where the lab is located. Contact the Technical Director if you do not have the required authorization.

The satellite Facility in the Billings Hospital
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 fro 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.

Acknowledgment of Scientific Work in Core Facilities

(Ful text on the OSRF Policy Page)

Core facility personnel are scientists. When they make a substantial intellectual and/or experimental contribution to a publication, they deserve to be acknowledged.

The existence of core facilities depends in part on proper acknowledgment in publications. This is an important metric of the value of most core facilities. Proper acknowledgment of core facilities enables them to obtain financial and other support so that they may continue to provide their essential services in the best ways possible. It also helps core personnel to advance in their careers, adding to the overall health of the core facility.

Core facilities should always be included in the acknowledgment section of publications which include contributions from said core facilities. Such contributions could include:

  • Paid technical help
  • Writing assistance
  • Financial and material support
  • Scientific advice

Furthermore, funding sources for Core Facilities, such as the Comprehensive Cancer Center Grant, may require acknowledgement specifically.

To help us tracking acknowledgments, we ask that you include the RRID number of the Facility (SCR_017760).

Examples of acknowledgments

[Technique/technology] was performed by the [facility name] at University of Chicago, which receives financial support from [sponsor name (grant number)]. RRID: SCR_017760

We thank The University of Chicago [facility name], especially [staff name], for their assistance with [technique/technology]. RRID: SCR_017760


Contributions from resource scientists that involve novel resource laboratory work and insight, experimental design, or advanced data analysis that make a publication possible or significantly enhance its value require co-authorship as the appropriate acknowledgment. Each author should participate at a level that enables s/he to accept responsibility for the content of the manuscript. Activities for which authorship is recommended:

  • Conception or design of project, including critical input and/or original ideas
  • Data acquisition, analysis and/or interpretation beyond routine practices
  • Critical drafting and/or revision of manuscript for intellectual content purposes
Damage to Core Instrumentation Policy

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.

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.