Flow Cytometry


Located in the Morrison Center, the Flow Cytometry Core Facility provides the following:

Comprehensive Data Collection and Analysis

Cell Sorting

Multi-Parameter Panel Design Assistance

Education and Training in Flow Cytometry

Application Consultation

Hours: Monday-Friday 9:00 am-5:00 pm or by appointment

Service Fees

Internal Users

  • Unassisted Analysis - $37/hour
  • Assisted Analysis - $63/hour
  • Sort - $52/hour
  • Sorter Set Up - $63
  • Training - $37/hour

External Users

  • Assisted Analysis - $125/hour
  • Unassisted Analysis - $110/hour
  • Sort - $115/hour
  • Sorter Set Up - $100

Usage is billed in 15 minute increments, and there is a 30 minute minimum charge for all appointments.


Cancellations/Missed Appointments– Users who have scheduled time may cancel up to 24 hours in advance of their start time. If users do not show up for a scheduled appointment, or cancel within 24 hours of the appointment, they will be billed for the scheduled amount of time.

Late Arrivals – Users will be billed for the amount of time they have reserved. If users arrive late, the billing time will start at the beginning of the scheduled appointment.

Training – All new users will participate in one or more training sessions with Core Facility staff. New users within an experienced lab may be instructed by trained personnel in the lab, but prior to being able to run samples by themselves, they will also be required to participate in a training session with Service Center staff.

After hours / Weekend Use – The Core Facility is open Monday – Friday, from 8am – 5pm. Trained users may be allowed access to the facility after hours and on weekends, after they have been given approval from the Core Facility Director. Please inform Director of any plans to work outside of normal lab hours.

Radioactive Materials – Radiolabeled samples are not permitted in the Core Facility.

Acknowledgements – Please acknowledge the Flow Cytometry Core Facility in any grant application or publication in which equipment and/or staff expertise was provided. Also, please send the Core Facility Director a copy of accepted publications containing data generated in the facility.

Biosafety – In an effort to decrease possible infection risk to Core Facility staff and lab users, we require that all samples be fixed prior to analysis. We are aware that certain applications preclude the fixing of samples. Should there be experimental reasons that your protocol is not compatible with fixation, please discuss this with Core Facility staff before running samples so appropriate handling and containment can be implemented.


Beckman Coulter CytoFLEX LX

The CytoFLEX LX is equipped with four lasers (405, 488 561 and 638nm), and is capable of detecting FSC, SSC and 16 colors. It operates under CytExpert Software.

Fluorofinder Panel Builder

Beckman Coulter Cytoflex l x System

NanoFCM NanoAnalyzer

The NanoAnalyzer is equipped with two lasers (488 and 640nm), and is capable of detecting SSC and two colors. It operates under NF Professional Software. The system is designed to measure the size and concentration of nanoparticle samples.
Beckman Coulter Cytoflex l x System


The Core Facility’s Aria is a four-laser platform (405, 488, 561 and 642nm) instrument capable of detecting FSC, SSC and 17-colors. It is the Center’s only instrument capable of sorting samples. It is able to sort up to four separate populations from the same sample, at a rate of up to 30,000 events/second. It is stationed in a Baker BioPROTECT biosafety cabinet. It operates under BD FACSDiva Software.

Fluorofinder Panel Builder


Instrument Reservations

Check the calendar below and then submit a request to use an instrument.

If you are having issues viewing this calendar, simply try to refresh the page.  If the issue persists, you may need to try another browser.

Please note: Users will be billed for the amount of time they have reserved. If users arrive late, the billing time will start at the beginning of the scheduled appointment.


Dirk Anderson, Director
MOLR 160
Office Phone: 402-472-3129
Lab Phone: 402-472-3142
Email Dirk

Advisory Committee

Facility Advisory Group
The mission of the Facility Advisory Group is to provide guidance and feedback to the facility regarding the most effective use of its resources to meet research demands.

Amanda Ramer-Tait, PhD
Phone: (402) 472-7293
Email: aramer-tait2@unl.edu
Ramer-Tait Lab

Rodrigo Franco Cruz, PhD
Phone: 402-472-8547
Email: rfrancocruz2@unl.edu
Franco Cruz Lab

Jay Reddy, MVSc, PhD 
Phone: 402-472-8541
Email: nreddy2@unl.edu
Reddy Lab


Useful Links

NanoAnalyzer Publication List – A rapidly growing list of publications that have utilized the NanoFCM NanoAnalyzer System.

Purdue Cytometry Discussion List – Ongoing discussion platform related to a multitude of flow cytometry topics.

Fluorofinder – Experiment Design & Reagent Search Platform  After selecting “Build a Panel,” search for “University of Nebraska-Lincoln (UNL)” in order to use settings specific to the Service Center’s instruments.

Thermofisher Panel Builder - Tool designed by Thermofisher for designing multi-parameter flow cytometry panels.

The Daily Dongle – Archive of FlowJo related webinars and discussions. 

FlowJo YouTube Channel  Indepth video tutorials covering a wide range of FlowJo topics.

Flow Cytometry  A Basic Introduction by DeNovo Software – A useful introductory book discussing the basics of flow cytometry.

Optimized Multicolor Immunofluorescence Panels (OMIPs) – Peer-reviewed articles describing optimized multicolor panels. These are great resources to utilize when building new panels, as they show what antibodies and fluorochromes work well together for specific cell types.

Practical Flow Cytometry – By Howard Shapiro – This free download of the 4th edition of this text offers very detailed discussions related to hardware, software, and applications.

Fluorescence Spectrum Viewers

BD Fluoroscence Spectrum Viewer

Thermofisher Fluorescence Spectra Viewer

BioLegend Fluorescence Spectra Analyzer

Boilerplate Text

The Flow Cytometry Core Facility is a part of the Center for Biotechnology at the University of Nebraska – Lincoln. The Center provides users with instrumentation, support and technical service for cell sorting and analysis. The Core currently manages and maintains three analysis instruments for use, including a 4-laser/16 color Beckman Coulter CytoFLEX LX, a 2-laser/4-color BD FACS Array (532 and 635nm), a 4-laser/10-color Cytek DxP10 (407, 488, 561, and 637nm). The cell sorter is a 4-laser/17-color BD FACS Aria II (405, 488, 561, 642nm) is housed in a Baker BioProtect biosafefy cabinet making it possible to sort BSL2 samples. The Aria II is capable of sorting up to four populations at once at a rate of up to 30,000 events/second, and is equipped with an automatic arm to be used for sorting in multi-well plates or slides. The Core's Director, Dirk Anderson has over fifteen years of flow cytometry experience, in both academia and industry. Along with analysis and sorting, the Center also offers training, protocol development assistance, and data analysis. 


Abeyá MM, Metz GE, Franco CR, Correas I, Osorio FA, Echeverria MG. Equine arteritis virus cytopathic effect: caspase-dependent cell death as the major consequence observed. J Microbiol Exp. 2018;6(4):171-173.

Mandal S, Kang G, Prathipati PK, Fan W, Li Q, Destache CJ. Long-acting parenteral combination antiretroviral loaded nano-drug delivery system to treat chronic HIV-1 infection: A humanized mouse model study. Antiviral Research 2018. 156: 85-91.

Sarmirova S, Borsanyiova M, Benkoova B, Pospisilova M, Arumugam R, Berakova K, Gomolcak P, Reddy J, Bopegamage S. Pancreas of coxsackievirus-infected dams and their challenged pups: A complex issue. Virulence. 2019 Dec;10(1):207-221.

Raverdeau M, Christofi M, Malara A, Wilk MM, Misiak A, Kuffova L, Yu T,McGinley AM, Quinn SM, Massilamany C, Reddy J, Forrester JV, Mills KH. Retinoic acid-induced autoantigen-specific type 1 regulatory T cells suppress autoimmunity. EMBO Rep. 2019 May;20(5).

Alkheraif AA, Topliff CL, Reddy J., Massilamany C, Donis RO, Meyers G, Eskridge KM, Kelling CL. Type 2 BVDV N(pro) suppresses IFN-1 pathway signaling in bovine cells and augments BRSV replication. Virology. Jul 2018; 507: 123-134.

Walker LR, Engle TB, Vu H, Tosky ER, Nonneman DJ, Smith TLP, Borza T, Burkey TE, Plastow GS, Kachman SD, Ciobanu DC, Host genetics influences replication of Porcine circovirus 2, PLoS Genetics, Oct 31, 2018;14(10).

Shihabudeen Haider Ali MS, Cheng X, Moran M, Haemmig S, Naldrett MJ, Alvarez S, Feinberg MW, Sun X. LncRNA Meg3 protects endothelial function by regulating the DNA damage response. Nucleic Acids Res. 2019 Feb 20;47(3):1505-1522.

Wei W, Wiggins J, Hu D, Vrbanac V, Bowder D, Mellon M, Tager A, Sodroski J, Xiang SH. Blocking HIV-1 Infection by Chromosomal Integrative Expression of Human CD4 on the Surface of Lactobacillus acidophilus ATCC 4356. J Virol. 2019 Apr 3;93(8).

Daverey A, Levytskyy RM, Swenson S, Hayward SL, Stanke KM, Viana MP, Narasimhan M, Khalimonchuk O, Kidambi S. Depletion of mitochondrial protease OMA1 alters proliferative properties and promotes metastatic growth of breast cancer cells. Sci. Rep. 2019. 9, 14746.

Lin H, Li Q, Du Q, Wang O, Wang Z, Akert L, Carlson MA, Zhang C, Subramanian A, Zhang C, Lunning M, Li M, Lei Y. Integrated generation of induced pluripotent stem cells in a low-cost device. Biomaterial. 2019 Jan; 189:23-36.

Lin H, Du Q, Li Q, Wang O, Wang Z, Sahu N, Elowsky C, Liu K, Zhang C, Chung S, Duan B, Lei Y. A Scalable and Efficient Bioprocess for Manufacturing Human Pluripotent Stem Cell-Derived Endothelial Cells. Stem Cell Reports. 2018 Aug 14; 11(2) 454-469.

Li Q, Lin H, Rauch J, Deleyrolle LP, Reynolds BA, Viljoen HJ, Zhang C, Zhang C, Gu L, Van Wyk E, Lei Y. Scalable Culturing of Primary Human Glioblastoma Tumor-Initiating Cells with a Cell-Friendly Culture System. Scientific Reports 8, 3531 (2018).

Lin H, Du Q, Li Q, Wang O, Wang Z, Liu K, Elowsky C, Zhang C, Lei Y. A hydrogel-based bioprocess for scalable manufacturing of human pluripotent stem cells-derived neural stem cells. ACS Appl Mater Interfaces. 2018 Sep 5; 10(35):29238-29250.

Lin H, Qiu X, Du Q, Li Q, Wang O, Akert L, Wang W, Anderson D, Liu K, Gu L, Zhang C, Lei Y. Engineered Microenvironment for Manufacturing Human Pluripotent Stem Cell-Derived Vascular Smooth Muscle Cells. Stem Cell Reports. 2019 Jan 8; 12(1) 84-97.

Li Q, Lin H, Du Q, Liu K, Wang O, Evans C, Christian H, Zhang C, Lei Y. Scalable and physiologically relevant microenvironments for human pluripotent stem cell expansion and differentiation. Biofabrication. 10(2018) 025006.

Lin H, Du Q, Li Q, Wang O, Wang Z, Liu K, Akert L, Zhang C, Chung S, Duan B, Lei Y. Differentiating human pluripotent stem cells into vascular smooth muscle cells in three dimensional thermoreversible hydrogels. Biomater. Sci., 2019, 7 347-361.

Beltrán J, Wamboldt Y, Sanchez R, LaBrant EW, Kundariya H, Virdi KS, Elowsky C, Mackenzie SA. Specialized Plastids Trigger Tissue-specific Signaling for Systemic Stress Response in Plants. Plant Physiology. 2018 Oct; 178(2) 672-683.

Beltrán J, Wamboldt Y, Sanchez R, LaBrant EW, Kundariya H, Virdi KS, Elowsky C, Mackenzie SA. Distinct Plastids Trigger Local Signaling for Systemic Stress Response in Plants. 1 Jun 2018. DOI:10.2139/ssrn.3188331.

Kittana H, Gomes-Neto JC, Heck K, Geis AL, Segura Muñoz RR, Cody LA, Schmaltz RJ, Bindels LB, Sinha R, Hostetter JM, Benson AK, Ramer-Tait AE. Commensal Escherichia coli Strains Can Promote Intestinal Inflammation via Differential Interleukin-6 Production. Front Immunol. 2018; 9 2318.

Guinn ZP, Petro TM. IFN-γ synergism with poly I:C reduces growth of murine and human cancer cells with simultaneous changes in cell cycle and immune checkpoint proteins. Cancer Letters, 2018 Dec 1; 438 1-9.

Chen Y, Wan Y, Wang N, Yuan Z, Niu W, Li Q, Guo J. Controlling the Replication of a Genomically Recoded HIV‑1 with a Functional Quadruplet Codon in Mammalian Cells. ACS Synth Biol. 2018 Jun 15; 7(6):1612-1617.