Bindley Bioscience Center

Frequently Asked Questions

How do I schedule time on the FC500 Flow Cytometers?

  • Contact Jill Hutchcroft ( to schedule a meeting to discuss your project needs and estimate costs.
  • All new applications should be discussed with the Flow Cytometry Facility staff before scheduling your experiment.
  • Contact Jill Hutchcroft ( to schedule mandatory laboratory training and training on the analysis instruments.
  • NOTE: Training will be billed at the regular hourly rate.

What guidelines should I follow when I design my experiment?

A great read here 10 Steps to a Successful Flow Cytometry Experiment

How do I schedule a cell sort on the Sony iCyt Reflection Cell Sorter?

  • All new sorts and sorting applications must be discussed with the Flow Cytometry Facility staff before scheduling your experiment.
  • All sorts will be performed by the Bindley Bioscience Center Flow Cytometry Facility staff.
  • Contact the Flow Cytometry Facility Manager to schedule a meeting to discuss your project needs and estimate costs.
  • You must send an email to Jill Hutchcroft to request a cell sorting appointment.

I am having problems scheduling time on the FC500. What should I do?

You must be trained and qualified to schedule time and to run samples on the instruments. If you have been trained and are still having problems, contact Jill Hutchcroft. Training will be billed at the regular hourly rate.

What do I need to know before contacting the staff to schedule a sort?

  • The fluorescent probes to be used in the experiment
  • The size of the cells to be sorted
  • The number of populations to be sorted
  • Whether the sorted sample should be kept sterile
  • Whether the sorting sample is a biohazard

What do I need to bring the day of the sort?

Have your cells suspended in a media that is ~5% protein, at a concentration of approximately 1-5 million cells/ml

Prepare receiving tubes containing 1+ ml of desired media. These tubes can be either 12X75mm or 15ml conical tubes.

You must prepare control samples. Negative controls are critical for setting up a sort.

Also, you must prepare single color fluorescent stained cells of each flourescent probe to be used. There must be a significant and bright population of positive cells to properly setup the sorter.

Do you offer sterile or live cell sorting?
Yes.  You will need to indicate that your sort needs to be sterile when you contact the Facility staff to schedule a sort.

Will flourochromes X and Y work together?

Check out our Spectral Viewer Tool

How do I properly compensate my multicolor flow samples?

How to do Flow Cytometry Compensation

Four steps must be taken to assure proper compensation. These steps should be taken with every experiment where the cell types differ, where the reagents differ, or where any instrument settings change--daily compensation is thus probably not frequent enough!

(1) The compensation tube must consist of cells that are unstained as well as cells that are singly-stained with the fluorescent probes. The stained (positive) cells must have the same autofluorescence (when they are unstained) as do the unstained (negative) cells in the compensation tube (e.g., all are lymphocytes).

(2) The PMT voltages must be set high enough guarantee that the negative population is off the axis in every channel.

(3) An analysis gate is set so that only cells with identical autofluorescence characteristics are viewed (e.g., a lymphocyte gate). An analysis gate is also set to include all of the negative cells and all of the positive cells.

(4) The centers of the positive and negative cell populations are aligned by matching the median fluorescences.

Source: Mario Roederer PhD

What flow cytometry data analysis software does the core have?
We have MXP, ModFit, WinList Version 6.0, and FlowJo.

All of these programs are available FREE of charge on the dedicated data analysis workstation in Bindley 233.  No appointment is required. 

How will I be billed?

We bill users for actual time spent on prepping and running the instruments for their project. We bill users at the labor rate for technician time spent on data acquisition. Consultation with users and assistance with data analysis are also billed at the labor rate.

NOTE: Training will be billed at the regular hourly rate.

What is the publication policy of the core?

Expectations for authorship for Core personnel will be discussed with initial Core contact. While authorship is not required and will often be inappropriate for Core personnel providing research input to the project, if there is significant intellectual and/or organizational effort of Core personnel to the work described in the manuscript, authorship is warranted and expected. For example, expert data analysis from Core personnel that is required in support of claims in a manuscript or patent warrant authorship. It will be made clear to investigators utilizing the Core that the recovery of Core expenses through the Core cost recovery system does not exclude the possibility for authorship for Core research personnel. Similarly, authorship does not substitute for payment of Core expenses for services rendered.

In publications that describe research that took place at the Core facility, authors should include a statement acknowledging the use of the facility and the Bindley Bioscience Center. All publications resulting from services provided by the FCCSF and supported by funding from the CTSI must acknowledge the CTSI and the Bindley Bioscience Center:

“The author(s) acknowledge the use of the Flow Cytometry and Cell Separation Facility of the Bindley Bioscience Center. This work was supported, in part, by grant NIH/NCRR RR025761.”

Bindley Bioscience Center -- Room 233
Purdue University
West Lafayette, IN 47907-1971

Flow Cytometry Facility

Jill Hutchcroft