Cytometry and Antibody Technology

Staff Assistance

Experiment Troubleshooting

If you are having trouble getting good quality data, please contact us! We are available to assess the issue, determine problem area(s) and suggest a solution. Examples of this include:

  • Sample preparation – tissue digestion and antibody/dye staining
  • Panel design
  • Instrument settings (voltages)
  • Compensation

Please contact Laura Johnston and/or David Leclerc to schedule a time to meet. The first meeting is free of charge! If subsequent meetings are needed, it is likely that we will charge the consultation fee ($35/hour). This will be discussed prior to billing.

Project Management

The Scientific Associate Director is available to support your research projects on any platform in the facility. The level of assistance can vary, it’s up to you to decide how much assistance to request. Some users only have a single meeting while others hire the Scientific Associate Director for the full range of services including staining the samples and analyzing the data. Please note that full service projects are taken on a case-by-case basis.

The consultation service is offered at an hourly rate of $35 for any of the topics outlined below. Please email Laura Johnston to schedule a meeting. If an initial meeting is needed to assess the scope of the project the consultation fee will be waived.

Panel Design

The Scientific Associate Director can design custom panels for all of our benchtop analyzers and sorters. This service may include:

  • Assigning fluorophores to a list of markers provided by the user
  • Rearranging an existing panel to improve data quality
  • Assigning fluorophores to markers to expand an existing panel
  • Combining smaller panels into one larger panel

On occasion, the Associate Scientific Director may suggest the addition of markers to identify common immune cell subsets of interest. However users are typically responsible for picking their markers of interest.

Any users who have designed their own panels are welcome to send the Scientific Associate Director their panels for a cursory review – this is free of charge.

Sample preparation and experimental design

The Scientific Associate Director can provide guidance on sample preparation and designing the experiment with appropriate controls. This may include:

  • Tissue digestion protocol
  • Staining protocol
  • Design of compensation controls/reference controls
  • Use of fluorescence minus one (FMO) controls, isotype controls, etc.
Data analysis and presentation

Once data has been acquired, the Scientific Associate Director can work with the user to create a custom analysis specific to the user’s project and hypothesis. This may include:

  • Checking data, panel, and compensation/spectral unmixing quality
  • Identifying cell populations of interest and differences in experimental groups
  • Determining the best method to present the findings
  • Generating publication-quality figures

Drop-Off Sample Service

You can have a member of the CAT Facility run your samples on your behalf on benchtop analyzers and multiplexing instruments.

The CAT Facility can run fully prepared samples on any of the benchtop analyzers – this is often referred to as “drop off samples”. No training is required for this service. However, those who are new to flow cytometry may find the Flow Basics Course informative and all are welcome to attend it. We also encourage you to read the new users page if you have never used our facility.

If you are new to flow cytometry it is recommended that you meet with the staff to discuss your experiment prior to dropping off any samples. This will ensure that you have appropriate panel design, sample staining protocol, controls, and analyzer selection.

Each time you schedule a benchtop analyzer for staff assisted drop off samples please follow these instructions:

    • Plan ahead. Our benchtop analyzers are often fully booked 3 days in advance, planning ahead will allow you to select your preferred time and analyzer.
    • Make an appointment in the iLab scheduler during normal operating hours (typically 9AM-5PM Mon-Fri). In the reservation popup window, write “drop off samples” in the event notes text box (left side) and complete the drop off sample form (right side, select “yes” checkbox to view)
    • Inform the staff of your reservation by emailing CATHelp@bsd.uchicago.edu at least 24 hours prior to your scheduled time. Example text: I have scheduled the {name of analyzer} on {date and time of appointment}, is anyone available to run my samples for me?. Please email the staff prior to every appointment. The staff will modify your appointment if no one is available.

After the staff has run the samples you will receive:

    • The FCS data files
    • The basic analysis of your data on the analysis platform of your choice

The CAT Facility staff can prepare the plate according to the protocol included in the kit and process the plate on the instrument. Please contact CATHelp@bsd.uchicago.edu to discuss your project.

You will receive

  • The raw data
  • The calculated concentrations based on the readout of the standard curve