Flow Cytometry and Cell Sorting

The mission of the Flow Cytometry Core at Penn State College of Medicine is to facilitate cutting-edge research by providing state-of-the-art fluorescence-activated cell sorting and analytical services at reasonable hourly rates. To achieve these goals, the facility provides three full-time staff and a faculty director to help investigators with all aspects of data collection including experiment design.

In addition, the following flow cytometers are available for use by investigators at Penn State Cancer Institute and Penn State College of Medicine:

  • 4-color FACSCalibur
  • 10-color FACSCanto
  • 16-color LSR II
  • 16-color LSR Fortessa
  • 17-color BD FACS Aria SORP high-performance cell sorter

Part of the core also serves as a CAP-certified lab and provides instrumentation and services to the various clinical labs of Penn State Health Milton S. Hershey Medical Center.

Investigators are asked to review the information on this page to ensure their flow cytometry experiments are conducted using appropriate methods and techniques to produce the most accurate data in a cost-efficient manner.

Submit cell sorting experiment form

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Instrumentation and Services

Flow Cytometry Overview Expand answer

Flow cytometry is a means of identifying and measuring certain physical and chemical characteristics of cells or particles as they travel in suspension one by one past a sensing point. The flow cytometer is able to “look” at thousands of cells or particles per second and perform and record many simultaneous measurements for each cell or particle.

The flow cytometer consists of a light source, collection optics, electronics and a computer to translate signals to data. The light source of choice is usually a laser, which emits coherent light at a specified wavelength. Scattered and emitted fluorescent light is collected by two lenses (one set in front of the light source and one set at right angles) and by a series of optics, beam splitters and filters, specific bands of fluorescence can be measured.

A flow cytometer can measure physical characteristics such as cell size, shape and internal complexity and, of course, any cell component or function that can be detected by a marker attached to a fluorescent compound can be examined. A number of these cell markers and measurements can be made for each cell and combined to give an informative summary of the characterization, identification and function of large populations of cells. So the applications of flow cytometry are numerous, and this has led to the widespread use of these instruments in the biological and medical fields.

Some of the more common research applications include: immunology, cell cycle and cell growth, cell function and activation, cell differentiation, apoptosis, platelet activation, toxicology and green fluorescent protein detection.

Some of the common clinical studies include: leukemia and lymphoma characterization, immune studies such as T and B cell subset determinations, stem cell content monitoring for transplant, nuclear ploidy and cell cycle determinations and reticulocyte counting.

In addition to analyzing populations of cells and particles for information and data which can be stored electronically and displayed in the form of dot plots and histograms, some flow cytometers have the ability to physically sort out cells or particles of interest. These cells can be sorted out of a heterogeneous mixture into a very pure population for further studies.

BD FACSCalibur Expand answer

Laser excitation wavelengths (two)

  • Blue: 488nm
  • Red: 635nm

Fluorescence detection (four)

  • Blue: 530nm, 585nm, 650nm
  • Red: 670nm
BD FACSCanto (10-color) Expand answer

Laser excitation wavelengths (three)

  • Blue: 488nm
  • Red: 635nm
  • Violet: 405nm

Fluorescence detection (10)

  • Blue: 530nm, 575nm, 695nm, 780nm
  • Red: 670nm, 712nm, 780nm
  • Violet: 450nm, 525nm, 605nm

Canto 10 Fluorochrome Choices

BD-recommended color combinations:

  • Six-color: FITC, PE, PERCP-CY5.5, PE-CY7, APC, APC-CY7
  • Eight-color: FITC, PE, PERCP-CY5.5, PE-CY7, APC, APC-CY7, AMCYAN or V500, V450

Note: Alexa dye numbers are named using excitation wavelength whereas E Fluor and BD V dyes are named using emission wavelengths.

Revised: March 14, 2016

BD FACSAria SORP Expand answer

Laser excitation wavelengths (four)

  • Blue: 488nm
  • Red: 635nm
  • Violet: 405nm
  • Green: 532nm

Fluorescence detection (16)

  • Blue: 525nm, 582nm, 710nm
  • Red: 670nm, 730nm, 780nm
  • Green: 575nm, 610nm, 670nm, 710nm, 780nm
  • Violet: 450nm, 525nm, 610nm, 670nm, 710nm, 780nm

Using this equipment

Users are expected to accompany their samples and assist in the monitoring of data acquisition and sorting experiments. Core personnel will be responsible for all the setup and shutdown procedures related to each experiment. See details on the policies for using the FACSAria here.

The cell sorting experiment form must be submitted prior to scheduling a sort on the FACSAria.

FACSAria Fluorochrome Choices

These choices are arranged in the same order that the FACSAria software uses.

BD-recommended color combinations:

  • Six-color: FITC, PE, PERCP-CY5.5, PE-CY7, APC, APC-CY7
  • Eight-color: FITC, PE, PERCP-CY5.5, PE-CY7, APC, APC-CY7, AMCYAN or V500, V450
  • 10-color: FITC, PE, PE-Texas Red, PERCP-CY5.5, PE-CY7, APC, Alexa 680 or 700, APC-CY7, AMCYAN or V500, V450

Note: Alexa dye numbers are named using excitation wavelength whereas E Fluor and BD V dyes are named using emission wavelengths.

Revised: Oct. 27, 2017

Special Order BD LSR II Expand answer

Laser excitation wavelengths (four)

  • Blue: 488nm
  • Red: 635nm
  • Green: 532nm
  • Violet: 405nm

Fluorescence detection (15)

  • Blue: 525nm, 675nm
  • Red: 670nm, 730nm, 780nm
  • Green: 582nm, 616nm, 670nm, 710nm, 780nm
  • Violet: 450nm, 525nm, 610nm, 670nm, 710nm, 780nm

LSR II Fluorochrome Choices

BD-recommended color combinations:

  • Six-color: FITC, PE, PERCP-CY5.5, PE-CY7, APC, APC-CY7
  • Eight-color: FITC, PE, PERCP-CY5.5, PE-CY7, APC, APC-CY7, BV 421, BV 711
  • 10-color: FITC, PE, PE-Texas Red, PERCP-CY5.5, PE-CY7, APC, Alexa 680 or 700, APC-CY7, BV 421, BV 711

Note: Alexa dye numbers are named using excitation wavelength whereas E Fluor and BD V dyes are named using emission wavelengths.

Revised: Oct. 27, 2017

BD LSR Fortessa Expand answer

Laser excitation wavelengths (four)

  • Blue: 488nm
  • Red: 640nm
  • Green: 532nm
  • Violet: 405nm

Fluorescence detection (16)

  • Blue: 515nm, 695nm
  • Red: 670nm, 730nm, 780nm
  • Green: 585nm, 610nm, 670nm, 710nm, 780nm
  • Violet: 450nm, 525nm, 605nm, 655nm, 710nm, 780nm

Fortessa Fluorochrome Choices

BD-recommended color combinations:

  • Six-color: FITC, PE, PERCP-CY5.5, PE-CY7, APC, APC-CY7
  • Eight-color: FITC, PE, PERCP-CY5.5, PE-CY7, APC, APC-CY7, BV 421, BV 711
  • 10-color: FITC, PE, PE-Texas Red, PERCP-CY5.5, PE-CY7, APC, Alexa 680 or 700, APC-CY7, BV 421, BV 711

Note: Alexa dye numbers are named using excitation wavelength whereas E Fluor and BD V dyes are named using emission wavelengths.

Revised: Oct. 27, 2017

Instrument Configurations Expand answer

This table lists the Band Pass Filter for each instrument using the specified laser.

For the Blue 488nm laser on the Aria, configured to 515/20, a GFP/YFP filter set is available.

Revised: March 14, 2016

Procedures, Protocols and Forms

General Policies and Procedures Expand answer

The Flow Cytometry Core serves researchers at both Penn State Health Milton S. Hershey Medical Center and Penn State College of Medicine. There are three instruments (FACSCanto and two FACSCaliburs) dedicated to clinical use. Use of these machines by researchers are prohibited unless they are specifically directed to do so by the Core personnel. All other instruments, including the cell sorter, are for research use and must be scheduled in advance for use.

Billing for usage is done monthly according to Department and Principal Investigator. Billing is not broken down by technician or project, but if the researcher needs this information, it can be retrieved upon request to the core facility. All users must fill out the information page in Clarity LabLink LIMS each time they use equipment.

The facility is designed to have the users operate the instruments when running samples and analyzing data. Core personnel will train these users to become proficient over time in setting up their experiments, running samples and producing and archiving data resulting from the experiments.

There is a terabyte server available to all researchers to use for transferring data from the DIVA workstations to the individual laboratory for archival. This server space, available on the hersheymed.net network drive, is to be used only as a dropbox for later transfer to the investigator’s own archival system. Users may also transfer data to other portable storage media if desired. In any case, the user is ultimately responsible for archiving any and all data generated. DIVA workstations will only retain up to three months of work in the DIVA database and export folders. The research server is not a secure space to archive data, so again, the user is responsible to archive flow cytometry data, not the core.

Safety for all users and core personnel is a priority concern. Since the facility is a shared laboratory and is designated as a BSL-2 facility, there are certain guidelines that all users are responsible to be aware of and follow. This is a special concern for cell sorting, and biosafety concerns and guidelines will be strictly adhered to. This policy is summarized in the Safety Guidelines. This includes guidelines for the safe use of lasers as well.

Safety Guidelines Expand answer

The Flow Cytometry Core operates as a Biosafety Level 2 laboratory. These guidelines are reviewed and revised if necessary each year, and each facility user is responsible to review them on a regular basis to ensure they are in compliance. Occasionally, some cell sorting experiments may operate in the cell sorter room under BSL-2+ conditions. This will be determined by core staff.

General Safety

  1. Admission to the laboratory is restricted to authorized personnel when work with human samples or a known infectious agent is in progress.
  2. All cells must be assigned appropriate BSL levels for research use by the Biological Safety and Recombinant DNA Committee (Ralph Keil, PhD, Chair) before they are allowed to be used in the Flow Cytometry Core. Additional information can be found on the safety section of the Infonet (internal access only; login required).
  3. No BSL2+ samples are allowed to be run on the analyzers.
  4. Before any cell sorting experiment can be scheduled, the cell sorting experiment form must be completed. This allows time for appropriate evaluation of biohazards under high-speed sorting conditions. This must be done at least a week before the proposed experiment.
  5. Some unfixed, primary human and primate cells and other BSL2 cells to be used on the FACSAria High-Speed Cell Sorter may be designated as BSL2+ by the Flow Biosafety Committee. In these cases, strict adherence to the BSL2+ Standard Operating Procedures will be required (these procedures are located in the core). These same cells may be used under BSL2 conditions on the cell sorter if they are fixed according to accepted methods of inactivating all biohazards. (See Special Requirement for Sorting Primary Human Cells.)
  6. Whenever possible, samples of human or primate origin to be run on any cytometer should be fixed according to a process known and documented to inactivate HIV and other biohazards.
  7. All procedures must be performed carefully to minimize the creation of aerosols.
  8. All samples and time used on the instruments must be logged into the facility in Clarity LIMS. Samples that have been fixed for analyzing or sorting on the Cell Sorter may be monitored and recorded to ensure that the fixation is adequate.
  9. Work surfaces are to be decontaminated with 10 percent household bleach (FACS Clean) after any spillage of sample or hazardous material and after each user completes their work.
  10. Instrument decontamination shall be performed according to protocols posted on each instrument.
  11. All spills, however small, must be recorded in the accident book and reported to the lab manager.
  12. All liquid and solid waste and disposal is to be removed from the laboratory as biohazardous material by each user. This includes all nuclear staining reagents such as PI, EB, AO, etc.
  13. Gloves must be worn whenever handling or running biohazardous samples on the cytometer.
  14. Hands must be washed after handling biohazardous materials and before leaving the laboratory.
  15. Laboratory coats must be worn in the work area. These coats should be removed before leaving the laboratory.
  16. Neither syringes nor hypodermic needles should be used in the facility without the consent of the laboratory manager. Glass objects should only be used when absolutely necessary.
  17. No eating, drinking, smoking or applying cosmetics in the work area.
  18. No mouth pipetting.
  19. No animals are permitted within the laboratory.
  20. All biohazard samples must be transported to and from the core in double-sealed containers per College of Medicine safety policy.

Laser Safety

In addition to the above guidelines and because this facility uses Class 3a through Class 4 lasers, the following laser safety guidelines shall also be observed:

  1. Access to the laboratory will be limited to only those people necessary to the running of experiments when any laser is operating in the UV mode or when it is necessary to operate a laser without protective shielding.
  2. In such cases, the appropriate protective goggles or glasses will be made available and must be worn by those in the work area.
  3. Only qualified personnel shall operate or adjust any laser.

Any questions regarding these guidelines may be directed to the Flow Cytometry Core manager, Nate Sheaffer, at nas2@psu.edu or 717-531-6908, or to the director of the Flow Cytometry Core, Todd Schell, PhD, at tschell@pennstatehealth.psu.edu or 717-531-8169.

In the Event of a Potential Retrovirus Exposure

This item refers to exposure of skin or mucous membranes to infectious materials, and is modeled after the NIH program 3 Emergency Steps to Take in the Event of a Potential HIV Exposure.

The risk of infection is very dependent upon the titer of virus and the route of exposure. Thus, the risk of infection by contact of intact skin with infectious body fluids is probably truly zero, and although the risk of infection by contact of mucous membranes or non-intact skin with infectious body fluids may be extremely small, it is likely to be non-zero.

The three emergency steps are:

  1. Immediately initiate first aid at the work site.
    1. Contaminated skin should be meticulously cleaned for 10 minutes using a povidone iodine solution (such as Betadine) and copious amounts of water.
    2. Contaminated eyes and mucous membranes should be irrigated for five minutes using water.
  2. Notify your supervisor, if that person is immediately available. More importantly, go on to step 3.
  3. Report to the hospital emergency department to activate the invasive accident protocol (needle-stick protocol), which will include evaluation, counseling and provision of antiretroviral treatment if deemed appropriate. Do this immediately (i.e., within the half-hour).
FluoroFinder/Fluorochrome Specifications Expand answer


The FluoroFinder system allows researchers with experiment design using the College of Medicine’s flow cytometers.

FluoroFinder offers training videos:

Use Penn State’s FluoroFinder

Fluorochrome Specifications

BD Biosciences, makers of the flow cytometry equipment used at Penn State College of Medicine, has created a guide to its fluorochromes.

Search for “BD Biosciences Fluorochrome Specifications Chart” here

General Sample Requirements Expand answer


Cells must be brought in Falcon 12x75mm polystyrene test tubes (Falcon #2008) for running on any of the analyzers. Other tubes of varying sizes may be used on the cell sorter. Collection tubes for cell sorting should be polypropylene.

Volumes and Concentrations

Minimum sample volumes per tube are 0.5 ml. Cell concentrations should be 0.5 to 1.0 X 106 cells per ml.

Fluorochrome Selection

Investigators should review the capabilities of the instruments before selecting fluorochromes and dyes to ensure that the instruments can excite and detect the dyes of choice. For multicolor experiments, it is imperative to consult fluorochrome guidelines or personnel in the facility for best possible outcomes.

Compensation Controls

Investigators must bring positive and negative controls. A negative control is an unstained sample of cells in PBS or fixative or a sample of cells stained only with the secondary ab if this is the system being used. If samples are stained with more than one fluorochrome per test tube, investigators must bring in a sample stained with each fluorochrome individually. This is for compensation purposes.

If there are not enough positive stained cells for each fluorochrome, investigators may use antibody capture beads.

To make conclusions about the experiment, the proper controls are critical.

With questions or to learn what the appropriate controls are, call facility personnel at 717-531-6908.

Cell Staining Protocols Expand answer

Cell Surface Marker/Antigen Staining

For each control and test sample, prepare a single cell suspension of 1X106 cells in cold PBS. Wash cells once in at least 1 ml of PBS with 2 percent FBS/media, centrifuge cells and aspirate supernatant.

Resuspend cells in a final volume of 50μl containing the primary antibody at the correct titer and PBS with 2 percent FBS/media. Reference manufacturer’s guidelines but in general, incubate on ice or at room temperature for 20 to 30 minutes.

Wash cells twice in PBS with 2 percent FBS/media. Centrifuge and aspirate supernatant.

For a directly conjugated antibody, go to the next step. For indirect labeling, resuspend cell pellet in a final volume of 50μl containing the secondary antibody and PBS with 2 percent FBS/media.

Resuspend cells at a final concentration of 1 to 2 x 106 cells/ml in at least 0.4ml fresh 1 percent to 2 percent formaldehyde/PBS. Provide the proper controls and analyze by flow cytometry.

Cell Cycle

Two options are available:

  • PI staining of ETOH fixed cells for DNA content, cell cycle and apoptosis (easiest method)
  • PI staining of nuclei for DNA content and cell cycle (best resolution)

See protocols on intracellular staining and other methods here (UCLA).

Apoptosis Techniques

There are good commercial kits available. The core recommends using kits with Annexin V PE and 7AAD as the best fluorochrome combination.

Cell Sorting Requirements Expand answer

Cells should be concentrated to at least 5 million cells/ml. Investigators who want to sort lots of cells in a short amount of time may concentrate cells even more (but the more concentrated cells are, the more likely they might form clumps). Investigators should remember to calculate how many total cells will be needed to analyze in order to sort the required number of target cells after the sort experiment. In general, lymphocyte-sized cells can be run at rates close to 30K per second, and cell lines can be run around 12K per second.

Cell media must be brought in the tubes or trays into which the cells will be sorted. Tubes should be polypropylene to avoid static charges and can vary in size. Media should fill about one-third of the tube space before collection begins.

It is required that cells are filtered before sorting. Clogs will be a problem to any sorting experiment and increase biohazard risks. 35 or 40μm filter cap tubes are available from BD Biosciences for this purpose.

Also, investigators must read and adhere to the safety guidelines before sorting unfixed cells, and the cell sorting experiment form must be completed before any sorting experiment is scheduled. This form must be submitted for review one week prior to scheduling the sorting experiment.

If, after the core’s review of the cell sorting experiment form, it is determined that the experiment is at the BSL2+ level, the investigator will be required to read and adhere to the Flow Cytometry BLS2+ Standard Operating Procedures for cell sorting, which is available in the cell sorter room.

Special Requirement for Sorting Primary Human Cells Expand answer

Any request to sort live, primary human cells in the Flow Cytometry Core will require a review of the samples in question by the core director based on the information on the cell sorting experiment form and possible consultation with the principal investigator involved. (This does not necessarily apply to human cells that are from an established published cell line.)

Several outcomes of this evaluation are possible. Some high-risk populations may be deemed too high-risk to sort in this facility. Other populations may be sorted under BSL2 conditions, others under BSL2+ conditions, and still others only after the donors are tested for HIV antibody and Hepatitis C and B Core antibody.

If donor testing is required, investigators must contact the clinical trials coordinator for details on the testing process. Once tests are completed, a copy of the test report without patient ID will be signed by the requesting principal investigator and forwarded to the Flow Cytometry Core before the cell sorting experiment is performed.

Citation Expand answer

Investigators should cite Penn State College of Medicine Flow Cytometry Core and list the names of the instruments that were utilized either in the Materials and Methods section or the Acknowledgements section of any article. Examples are given here.

Materials and Methods

“Flow cytometric data were collected using an LSR II (Becton Dickinson) instrument in Penn State College of Medicine’s Flow Cytometry Core.”


“Live cells were sorted by flow cytometry under BSL-2 conditions using a FACSAria SORP (Becton Dickinson) instrument in Penn State College of Medicine’s Flow Cytometry Core.”


“We thank Nate Sheaffer and Joseph Bednarczyk from Penn State College of Medicine’s Flow Cytometry Core for assistance with flow cytometry analysis and cell sorting.”

Flow Cytometry Instrumentation

  • BD FACSCalibur (BD Biosciences, San Jose, CA)
  • BD FACSCanto (10-Color) (BD Biosciences, San Jose, CA)
  • BD LSR II (Special Order System) (BD Biosciences, San Jose, CA)

  • BD LSRFortessa (BD Biosciences, San Jose, CA)
  • BD FACSAria (Special Order Research Product) (BD Biosciences, San Jose, CA)
Other Flow Cytometry Resources Expand answer


Introductions to Flow Cytometry

Fluorochrome Choices and Controls

Cytoplasmic Staining Resources


Other Resources

Work With Flow Cytometry

Fees Expand answer

For information on fees, call core facility personnel at 717-531-6908.

Note: “No-shows” and cancellations less than eight hours in advance may be charged for scheduled time.

Scheduling Expand answer

General Usage

To see available times for use of the equipment in the Flow Cytometry Core, use the calendar here. The calendar is view-only and is updated frequently.

Scheduling time for sample acquisition or data analysis is done by calling the core at 717-531-6908. Researchers are scheduled on a first-come, first-served basis. Scheduling is best done a few days in advance to ensure that sufficient time is available and that samples will be able to run within a reasonable time after they have been prepared.

For time-course studies, it is best to check with the facility well in advance to ensure that someone will be there on the days access to the cytometers is needed. Occasionally, a request for live cell analysis will take priority over a previously scheduled time slot using fixed cells.

Requests for cell sorting must be made at least a week in advance to ensure assistance will be available and that all biosafety concerns can be addressed.

Off-Hours Usage

Because of the nature of certain research projects, it is sometimes necessary that accommodations be made for the processing of samples through the flow cytometers in the absence of the core personnel who normally set up the instruments and assist the users for data acquisition.

The Flow Cytometry Core has a specialist and a trained backup research associate to cover almost all of the normal business hours for research use. However, there are rare occasions when neither person will be available to assist users even during regular business hours. For this reason, it is necessary to consult the scheduling calendar well in advance to ensure that projects can be scheduled accordingly.

For times other than regular business hours (i.e., evenings or weekends), certain approved users will also be able to use the flow cytometers upon prior arrangement with core personnel. There is a keypad lock on the door, and the code will be made available for these users. These users will be completely on their own in starting up the instrumentation and shutting it down properly.

In the event that problems would arise, the operator has the option of calling the lab manager, Nate Sheaffer, at 717-571-6231 (cell phone). If he cannot be reached or the problem cannot be solved over the phone, it will be necessary to stop the processing of samples at that point and wait until core personnel return to the lab.

These special arrangements need to be scheduled ahead of time with the approval of core personnel.

To be approved for such off-hours data acquisition, investigators must see one core personnel to complete the necessary training checklist for the particular instrument that will be used. For any occasion to process samples when core personnel are not in the lab, only the Research FACSCalibur, FACSCanto II, LSR II and LSR Fortessa are available for research use. There are special arrangements for the other instruments to be made available for the processing of clinical specimens.

The FACSAria Cell Sorter will not be available for use in the absence of core personnel at any time.

Publications Expand answer
Contact the Core Expand answer