Flow Cytometry Shared Resource (FCSR)

The Flow Cytometry Shared Resource (FCSR) supports basic and translational research of University of Illinois Cancer Center members by providing a wide array of analytical spectral and traditional flow cytometry, single-cell mass cytometry, high-speed cell sorting services, and imaging flow cytometry. The FCSR also provides instrumentation for the detection of sub-cellular particles such as exosomes and extra-cellular vesicles and live cell metabolic flux studies. In addition, biomarker assay development for the detection of soluble proteins such as cytokines, chemokines, and phospho-proteins from biological samples via multiplex assays or ELISA is available. Services extend beyond basic techniques to include development of new antibody panels for mass cytometry and customized methods for cell sorting.

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Our Services

The FCSR offers multiple services including flow cytometry analysis on bench-top flow cytometers, cutting-edge mass and imaging cytometers, high-speed cell sorting, experimental design, and data analysis. 

Consultations and Collaborations

FCSR has an open-door policy and provides free consultations for designing experiments, reagents, and protocol optimization as well as support with experimental design and data analysis. Grant writing support as consultants or collaborations, contributions to manuscripts, and letters of support are also provided to UICC members.

Education and Training

The FCSR has hosted lectures on immunological methods with a focus on flow cytometry theory and hands-on instrument use. Lecture hours are devoted to immunological reagents and the theory behind flow cytometry and related techniques, followed by sample preparation, data acquisition and data analysis. Dissemination of information by the FCSR also occurs through regular seminars and workshops. For unassisted use, one-on-one training on all instruments with the exception of the mass cytometer and the cell sorters is provided.

Direct and Pipeline Services

Direct Services: Assisted acquisition and data analysis are provided to UICC users who desire expert acquisition and analysis of samples, particularly for complex, multi-parametric assays. This includes quality control setting up of voltages and gains by the FCSR staff, as well as data analysis using high-capability software platforms such as Cytobank and Kaluza.

Pipeline Services Performed in Collaboration with Other Shared Resources: To study the role of single cells in cancer, a pipeline for cell sorting, single cell transcriptomics/genomics, single cell data analysis, data interpretation, and bioinformatics is set up between the FCSR, CGSR, and CBSR.


  • Traditional flow cytometers
    • LSR Fortessa (4 lasers, 13-color)
    • CytoFLEX S (4 lasers, 13-color)
    • Gallios (3 lasers, 10-color)
  • Spectral flow cytometers
    • Aurora (5 lasers, up to 40-colors)
  • Mass Cytometer
    • Fluidigm Mass cytometer (CyTOF 2, upgraded to Helios)
  • Cell sorters
    • MoFlo Astrios- (5 lasers, 18-color and six-way sorting)
    • MoFlo Astrios EQ- (4 lasers, 14-color and six-way sorting)
  • Extracellular Vesicle/small Particle Research
    • Nanosight NS300- 488nm (detection of particles between 20-2000nm)
    • Zeta sizer Nano series
  • Biomarker Analysis
    • MagPix (for measuring cytokines, phosphoproteins from serum, supernatant, BAL, etc.)
    • SpectraMax M2 microplate/cuvette reader for spectrophotometry
  • Metabolic studies
    • SeaHorse XFe96
  • Data Analysis Platforms
    • Kaluza (site license), Cytobank, Modfit, CytExpert

Meet Our Team

Zainab Alshawabkeh, BS, Research Specialist

Zainab Alshawabkeh is experienced in flow cytometry and maintains and operates the instruments, and provides staff-assisted acquisition services for analytical flow cytometry and cell sorting.

Balaji Ganesh, PhD, FCSR Director

Dr. Ganesh is an immunologist and flow cytometrist with more than 17 years of experience in the field in high-parameter data design, acquisition, and analysis; responsible for facility oversight and overall administrative and scientific direction of the SR.

Wei Feng, MS, Research Specialist

Wei Feng’s background is in basic biology, helps to develop cutting-edge flow cytometric techniques and provides day-to-day management of the cell sorters, and provides staff-assisted runs on the mass cytometer. 

Recent Publications

Serikbaeva A, Li Y, Ganesh B, Zelkha R, Kazlauskas A. Hyperglycemia Promotes Mitophagy and Thereby Mitigates Hyperglycemia-Induced Damage. Am J Pathol. 2022 Dec;192(12):1779-1794. doi: 10.1016/j.ajpath.2022.08.004. Epub 2022 Sep 3. PubMed PMID: 36063899

Kumar S, Das S, Sun J, Huang Y, Singh SK, Srivastava P, Sondarva G, Nair RS, Viswakarma N, Ganesh BB, Duan L, Maki CG, Hoskins K, Danciu O, Rana B, Li S, Rana A. Mixed lineage kinase 3 and CD70 cooperation sensitize trastuzumab-resistant HER2+ breast cancer by ceramide-loaded nanoparticles. Proc Natl Acad Sci U S A. 2022 Sep 20;119(38):e2205454119. doi: 10.1073/pnas.2205454119. Epub 2022 Sep 12. PubMed PMID: 36095190; 

Bachmaier K, Stuart A, Singh A, Mukhopadhyay A, Chakraborty S, Hong Z, Wang L, Tsukasaki Y, Maienschein-Cline M, Ganesh BB, Kanteti P, Rehman J, Malik AB. Albumin Nanoparticle Endocytosing Subset of Neutrophils for Precision Therapeutic Targeting of Inflammatory Tissue Injury. ACS Nano. 2022 Mar 22;16(3):4084-4101. doi: 10.1021/acsnano.1c09762. Epub 2022 Mar 1. PubMed PMID: 35230826

Chen T, Sun MR, Zhou Q, Guzman AM, Ramchandran R, Chen J, Ganesh B, Raj JU. Extracellular vesicles derived from endothelial cells in hypoxia contribute to pulmonary artery smooth muscle cell proliferation in-vitro and pulmonary hypertension in mice. Pulm Circ. 2022 Jan;12(1):e12014. doi: 10.1002/pul2.12014. eCollection 2022 Jan. PubMed PMID: 35506070

Kumar P, Arbieva ZH, Maienschein-Cline M, Ganesh BB, Ramasamy S, Prabhakar BS. Induction of Antigen-Independent Proliferation of Regulatory T-Cells by TNF Superfamily Ligands OX40L and GITRL. Methods Mol Biol. 2021;2248:63-71. doi: 10.1007/978-1-0716-1130-2_4. PubMed PMID: 33185867.

Zhou B, Magana L, Hong Z, Huang LS, Chakraborty S, Tsukasaki Y, Huang C, Wang L, Di A, Ganesh B, Gao X, Rehman J, Malik AB. The angiocrine Rspondin3 instructs interstitial macrophage transition via metabolic-epigenetic reprogramming and resolves inflammatory injury. Nat Immunol. 2020 Nov;21(11):1430-1443. doi: 10.1038/s41590-020-0764-8. Epub 2020 Aug 24. PubMed PMID: 32839607

Qin S, Predescu DN, Patel M, Drazkowski P, Ganesh B, Predescu SA. Sex differences in the proliferation of pulmonary artery endothelial cells: implications for plexiform arteriopathy. J Cell Sci. 2020 May 14;133(9). doi: 10.1242/jcs.237776. PubMed PMID: 32409569

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