Flow Cytometry Core Facility
The Flow Cytometry Core Facility (FCCF) at the University Hospital Bonn offers advanced flow cytometry services, including cell analysis and sorting, to researchers across various disciplines. The facility is equipped with state-of-the-art instruments, such as the BD FACSDiscover™S8 cell sorter an ImageStream® MarkII and two Sony ID7000™spectral analyzers, as well as classical instruments like the BD FACSCanto™II and LSRFortessa™ a FACSAria™Fusion and FACSAria™III and other instruments (comprehensive list: Instrument). These tools enable comprehensive analysis of cellular characteristics and efficient sorting of specific cell populations for further study. Additionally, the FCCF provides training, consultation, and support in experimental design and data analysis, ensuring researchers can effectively utilize these technologies for their scientific investigations

Instruments
The Flow Cytometry Core Facility operates 14 different instruments in various performance classes and application areas.
We cover the full range from the classic 3-laser 8-color analyzer to the most sophisticated 7-laser spectral analyzer and image cytometer to the image-enabled spectral cell sorter BD FACSDiscover™ S8.

Services
The Flow Cytometry Core Facility provides a range of services to our users:
Cell sorting: Separation of specific cell populations for further analysis or experimentation. Cell sorting is provided as a full service with an operator. This cell sorting service is limited to standard office hours. Alternatively, advanced users can learn how to operate the Sony MA900™cell sorter.
Teaching
The Flow Cytometry Core Facility offers individual training courses on our analyzers and the Sony MA900™cell sorter as well as regular workshops to introduce you to flow cytometry, cell sorting or spectral flow cytometry in general or the basics of data analysis.
Dates for regular online trainings can be found at the event section of the BTC homepage.
Do you have any questions?
FAQs
Answers to frequently asked questions about the PPMS booking system, the billing of core facility services and much more can be found in our General FAQ section and specific sorting related Questions can be found under Sorter FAQs.
Consulting
Are you interested in our services? Please get in touch with the relevant contact person or send us an e-mail: fccf@uni-bonn.de
Acknowledgement
You would like to publish your results but do not know how to take the support of the Core Facility into account? Here you will find detailed instructions.
Needful Links
Acknowledgements:
1. Breßer, Mona; Siemens, Kevin D.; Schneider, Linda; Lunnebach, Jonah E.; Leven, Patrick; Glowka, Tim R. et al. (2025): Macrophage-induced enteric neurodegeneration leads to motility impairment during gut inflammation. In: EMBO molecular medicine 17 (2), S. 301–335. DOI: 10.1038/s44321-024-00189-w .
2. Eichhorn, Lars; Kleiner, Jan Lukas; Bartsch, Benedikt; Nazir, Mariam Louis Fathy; Zhang, Yunyang; Coburn, Mark et al. (2025): CCR2 dependent recruited pro-inflammatory monocytes contribute to the development of left ventricular hypertrophy in mice upon transverse aortic constriction. In: PloS one 20 (4), e0318407. DOI: 10.1371/journal.pone.0318407 .
3. Gohr, Florian N.; Christensen, Maria H.; Jenster, Lea-Marie; Tesfamariam, Yonas M.; Lapp, Dorothee J.; Mackenzie, Jason; Schmidt, Florian I. (2025): A novel reporter to visualize and quantify endogenous inflammasomes and caspase-1 recruitment.
4. Hansen, Aylin; Sanders, Christine; Fronhoffs, Florian; Funke, Kai; Kristiansen, Glen; Schorle, Hubert (2025): BRD9 inhibition as potential treatment option for testicular germ cell tumors. In: Andrology. DOI: 10.1111/andr.70038 .
5. Kaiser, Kim M.; Raabe, Jan; ToVinh, Michael; Hack, Gudrun; Ahmad, Sarah; Müller, Niko et al. (2025): IL-17A-producing NKp44(-) group 3 innate lymphoid cells accumulate in Familial Adenomatous Polyposis duodenal tissue. In: 2041-1723 16 (1), S. 3873. DOI: 10.1038/s41467-025-58907-y .
6. Kirchhoff, Alexander; Herzner, Anna-Maria; Urban, Christian; Piras, Antonio; Düster, Robert; Mahlberg, Julia et al. (2025): RNA-binding proteins hnRNPM and ELAVL1 promote type-I interferon induction downstream of the nucleic acid sensors cGAS and RIG-I. In: The EMBO Journal 44 (3), S. 824–853. DOI: 10.1038/s44318-024-00331-x .
7. Koch, Philipp; Zhang, Zijian; Genuth, Naomi R.; Susanto, Teodorus Theo; Haimann, Martin; Khmelinskaia, Alena et al. (2025): A versatile toolbox for determining IRES activity in cells and embryonic tissues. In: The EMBO Journal 44 (9), S. 2695–2724. DOI: 10.1038/s44318-025-00404-5 .
8. Mohamed, Adham Abuelola; Wallerath, Christina; Hunkler, Charlotte; Hartmann, Gunther; Stankovic, Sanda; Brooks, Andrew G.; Schlee, Martin (2025): RIG-I Stimulation Enhances Effector Function and Proliferation of Primary Human CD8 T Cells.
Co-Authorship:
1. Silva Ribeiro, Dalila Juliana; Yüksel, Seniz; Dolf, Andreas; Wachten, Dagmar (2024): Isolation and Flow Cytometry Analysis of Macrophages from White Adipose Tissue. In Methods in molecular biology (Clifton, N.J.) 2713, pp. 149–158. DOI: 10.1007/978-1-0716-3437-0_10 .
Acknowledgements:
1. Böhner, Alexander M. C.; Effland, Alexander; Jacob, Alice M.; Böhner, Karin A. M.; Abdullah, Zeinab; Brähler, Sebastian et al. (2024): Determining individual glomerular proteinuria and periglomerular infiltration in a cleared murine kidney by a 3-dimensional fast marching algorithm. In: Kidney international 105 (6), S. 1254–1262. DOI: 10.1016/j.kint.2024.01.043 .
2. Colón, David F.; Wanderley, Carlos W.; Turato, Walter M.; Borges, Vanessa F.; Franchin, Marcelo; Castanheira, Fernanda V. S. et al. (2024): Paediatric sepsis survivors are resistant to sepsis-induced long-term immune dysfunction. In: British journal of pharmacology 181 (8), S. 1308–1323. DOI: 10.1111/bph.16286 .
3. Frasconi, Teresa M.; Kurts, Christian; Dhana, Ermanila; Kaiser, Romina; Reichelt, Miriam; Lukacs-Kornek, Veronika et al. (2024): Renal IL-23-Dependent Type 3 Innate Lymphoid Cells Link Crystal-induced Intrarenal Inflammasome Activation with Kidney Fibrosis. In: Journal of immunology (Baltimore, Md. : 1950) 213 (6), S. 865–875. DOI: 10.4049/jimmunol.2400041 .
4. Guth, Cécile; Schumacher, Pia Philippa; Vijayakumar, Archena; Borgmann, Hannah; Balles, Helene; Koschel, Marianne et al. (2024): Eosinophils Are an Endogenous Source of Interleukin-4 during Filarial Infections and Contribute to the Development of an Optimal T Helper 2 Response. In: Journal of Innate Immunity 16 (1), S. 159–172. DOI: 10.1159/000536357 .
5. Hardt, Miriam; Mayr, Alexandra; Kutschera, Eric; Marciniak, Jana; Küchler, Erika Calvano; Kirschneck, Christian et al. (2024): Rho Kinases and Reactive Oxygen Species in Autophagy Regulation by Pressure in Periodontal Ligament Cells. In: Braz. Dent. J. 35, Artikel e24-5944. DOI: 10.1590/0103-6440202405944 .
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9. Kirchhoff, Alexander; Herzner, Anna-Maria; Urban, Christian; Piras, Antonio; Düster, Robert; Mahlberg, Julia et al. (2024): RNA-binding proteins hnRNPM and ELAVL1 promote type-I interferon induction downstream of the nucleic acid sensors cGAS and RIG-I. In: The EMBO Journal. DOI: 10.1038/s44318-024-00331-x .
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13. Rottmann, Sophia; Lukacs-Kornek, Veronika (2024): Isolation, Purification, and Comprehensive Flow Cytometry Assessment of Lung Stromal Cells. In: Current protocols 4 (12), e70078. DOI: 10.1002/cpz1.70078 .
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17. Silva Ribeiro, Dalila Juliana; Yüksel, Seniz; Dolf, Andreas; Wachten, Dagmar (2024): Isolation and Flow Cytometry Analysis of Macrophages from White Adipose Tissue. In: Methods in molecular biology (Clifton, N.J.) 2713, S. 149–158. DOI: 10.1007/978-1-0716-3437-0_10.
18. Surendar, Jayagopi; Hackenberg, Roslind K.; Schmitt-Sánchez, Fabio; Ossendorff, Robert; Welle, Kristian; Stoffel-Wagner, Birgit et al. (2024): Osteomyelitis is associated with increased anti-inflammatory response and immune exhaustion. In: Frontiers in immunology 15, S. 1396592. DOI: 10.3389/fimmu.2024.1396592 .
19. van Baarle, Lies; Simone, Veronica de; Schneider, Linda; Santhosh, Sneha; Abdurahiman, Saeed; Biscu, Francesca et al. (2024): IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancer. In: Nat Commun 15 (1), S. 6079. DOI: 10.1038/s41467-024-50438-2 .
20. Weiss, Felix D.; Alvarez, Yubell; Shakeri, Farhad; Sahu, Anshupa; Leka, Petro; Dernst, Alesja et al. (2024): Retention of ES cell-derived 129S genome drives NLRP1 hypersensitivity and transcriptional deregulation in Nlrp3tm1Flv mice. In: Cell death and differentiation 31 (12), S. 1717–1729. DOI: 10.1038/s41418-024-01379-2 .
21. Xiao, Hongkui; Ulmert, Isabel; Bach, Luisa; Huber, Johanna; Narasimhan, Hamsa; Kurochkin, Ilia et al. (2024): Genomic deletion of Bcl6 differentially affects conventional dendritic cell subsets and compromises Tfh/Tfr/Th17 cell responses. In: Nat Commun 15 (1), S. 3554. DOI: 10.1038/s41467-024-46966-6 .
22. Mangan, Matthew S. J.; Akbal, Anil; Rivara, Sophie; Schröder, Agnes; Horvath, Gabor; Walch, Philipp et al.: Cytosolic sodium accumulation is a common danger signal triggering endocytic dysfunction and NLRP3 inflammasome activation: bioRxiv. Online verfügbar unter https://www.biorxiv.org/content/10.1101/2024.03.26.586774v2, zuletzt geprüft am 22.11.2024.
23. Marques Palma, Luisa; Schlaweck, Sebastian; Flores, Chrystel; Aslan, Hasan; Brossart, Peter; Kurts, Christian et al.: Chemokine Dynamics after Mrna Vaccination: Social Science Research Network (4914051), zuletzt geprüft am 22.11.2024.
24. Messmer, Julia M.; Thommek, Calvin; Piechutta, Manuel; Venkataramani, Varun; Wehner, Rebekka; Westphal, Dana et al.: T lymphocyte recruitment to melanoma brain tumors depends on distinct venous vessels. In: 1074-7613 57 (11), 2688‐2703.e11. DOI: 10.1016/j.immuni.2024.09.003 .
25. Oberkircher, Lara M.; Scheiding, Victoria M.; Rafeld, H. Linda; Hanssen, Eric; Hansen, Jan N.; Fleischmann, Markus J. et al.: Opposing roles of resident and infiltrating immune cells in the defense against Legionella longbeachae via IL-18R/IFN-γ/ROS axis in mice. In: 1933-0219 17 (5), S. 777–792. DOI: 10.1016/j.mucimm.2024.05.001 .
26. Salzmann, Rebekka J. S.; Krötz, Christina; Mocan, Tudor; Mocan, Lavinia P.; Grapa, Cristiana; Rottmann, Sophia et al.: Increased type-I interferon level is associated with liver damage and fibrosis in primary sclerosing cholangitis. In: 2471-254X 8 (3), e0380. DOI: 10.1097/HC9.0000000000000380 .
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28. Theodorou, Maria Rafailia; Yu, Jiangyan; Nikolka, Fabian; Zurkovic, Jelena; Wientjens, Chantal; Weiss, Patricia et al.: Anabolic lipid metabolism regulates adipose type 2 innate lymphoid cell differentiation to maintain metabolic health: bioRxiv. Online verfügbar unter https://www.biorxiv.org/content/10.1101/2024.03.26.586766v1, zuletzt geprüft am 22.11.2024.
29. Wurnig, Silas L.; Huber, Max E.; Weiler, Corinna; Baltrukevich, Hanna; Merten, Nicole; Stötzel, Isabel et al.: A fluorescent probe enables the discovery of improved antagonists targeting the intracellular allosteric site of the chemokine receptor CCR7: bioRxiv. Online verfügbar unter https://www.biorxiv.org/content/10.1101/2024.08.27.607356v1, zuletzt geprüft am 22.11.2024.
Co-Authorship:
1. Liter Silva Ribeiro, D.J., Yüksel, S., Dolf, A., and Wachten, D. (2024). Isolation and Flow Cytometry Analysis of Macrophages from White Adipose Tissue. In Tissue-Resident Macrophages: Methods and Protocols Methods in Molecular Biology., E. Mass, ed. (Springer US), pp. 149–158. 10.1007/978-1-0716-3437-0_10 .
Acknowledgements:
1. Funke, Kai; Einsfelder, Ulf; Hansen, Aylin; Arévalo, Lena; Schneider, Simon; Nettersheim, Daniel et al. (2023): Genome-scale CRISPR screen reveals neddylation to contribute to cisplatin resistance of testicular germ cell tumours. In: British journal of cancer 128 (12), S. 2270–2282. DOI: 10.1038/s41416-023-02247-5 .
2. Hackstein, Carl-Philipp; Spitzer, Jasper; Symeonidis, Konstantinos; Horvatic, Helena; Bedke, Tanja; Steglich, Babett et al. (2023): Interferon-induced IL-10 drives systemic T-cell dysfunction during chronic liver injury. In: Journal of hepatology 79 (1), S. 150–166. DOI: 10.1016/j.jhep.2023.02.026 .
3. Jenster, Lea-Marie; Lange, Karl-Elmar; Normann, Sabine; vom Hemdt, Anja; Wuerth, Jennifer D.; Schiffelers, Lisa D. J. et al. (2023): P38 kinases mediate NLRP1 inflammasome activation after ribotoxic stress response and virus infection. In: The Journal of experimental medicine 220 (1). DOI: 10.1084/jem.20220837 .
4. Klümper, Niklas; Ralser, Damian J.; Ellinger, Jörg; Roghmann, Florian; Albrecht, Julia; Below, Eduard et al. (2023): Membranous NECTIN-4 Expression Frequently Decreases during Metastatic Spread of Urothelial Carcinoma and Is Associated with Enfortumab Vedotin Resistance. In: Clinical cancer research : an official journal of the American Association for Cancer Research 29 (8), S. 1496–1505. DOI: 10.1158/1078-0432.CCR-22-1764 .
5. Raabe, Jan; Kaiser, Kim M.; ToVinh, Michael; Finnemann, Claudia; Lutz, Philipp; Hoffmeister, Christoph et al. (2023): Identification and characterization of a hepatic IL-13-producing ILC3-like population potentially involved in liver fibrosis. In: Hepatology (Baltimore, Md.) 78 (3), S. 787–802. DOI: 10.1097/HEP.0000000000000350 .
6. Regt, Ann Kristin de; Anand, Kanchan; Ciupka, Katrin; Bender, Felix; Gatterdam, Karl; Putschli, Bastian et al. (2023): A conserved isoleucine in the binding pocket of RIG-I controls immune tolerance to mitochondrial RNA. In: Nucleic acids research 51 (21), S. 11893–11910. DOI: 10.1093/nar/gkad835 .
7. Tsukamoto, Yuta; Hiono, Takahiro; Yamada, Shintaro; Matsuno, Keita; Faist, Aileen; Claff, Tobias et al. (2023): Inhibition of cellular RNA methyltransferase abrogates influenza virus capping and replication. In: Science (New York, N.Y.) 379 (6632), S. 586–591. DOI: 10.1126/science.add0875 .
8. Tzaridis, Theophilos; Weller, Johannes; Bachurski, Daniel; Shakeri, Farhad; Schaub, Christina; Hau, Peter et al. (2023): A novel serum extracellular vesicle protein signature to monitor glioblastoma tumor progression. In: International journal of cancer 152 (2), S. 308–319. DOI: 10.1002/ijc.34261 .
9. Colón, David F.; Wanderley, Carlos W.; Turato, Walter M.; Borges, Vanessa F.; Franchin, Marcelo; Castanheira, Fernanda V. S. et al.: Paediatric sepsis survivors are resistant to sepsis-induced long-term immune dysfunction. In: 1476-5381 181 (8), S. 1308–1323. DOI: 10.1111/bph.16286 .
10. Frasconi, Teresa M.; Kurts, Christian; Dhana, Ermanila; Kaiser, Romina; Reichelt, Miriam; Lukacs-Kornek, Veronika et al.: Renal IL-23–Dependent Type 3 Innate Lymphoid Cells Link Crystal-induced Intrarenal Inflammasome Activation with Kidney Fibrosis. In: 0022-1767 213 (6), S. 865–875. DOI: 10.4049/jimmunol.2400041 .
11. Heuser-Loy, Christoph; Baumgart, Ann-Kathrin; Hackstein, Carl-Philipp; Courrèges, Christina J. F.; Philipp, Marie-Sophie; Thaiss, Christoph A. et al.: Conditional NKT Cell Depletion in Mice Reveals a Negative Feedback Loop That Regulates CTL Cross-Priming. In: 0022-1767 212 (1), S. 35–42. DOI: 10.4049/jimmunol.2300662 .
Co-Authorship:
1. Steinhoff, C., Pickarski, N., Litt, T., Hajdas, I., Welte, C., Wurst, P., Kühne, D., Dolf, A., Germer, M., and Kallmeyer, J. (2022). NEW APPROACH TO SEPARATE AND DATE SMALL SPORES AND POLLEN FROM LAKE SEDIMENTS IN SEMI-ARID CLIMATES. Radiocarbon 64, 1191–1207. 10.1017/RDC.2022.34.
Acknowledgements:
1. Arévalo, Lena; Merges, Gina Esther; Schneider, Simon; Oben, Franka Enow; Neumann, Isabelle Sophie; Schorle, Hubert (2022): Loss of the cleaved-protamine 2 domain leads to incomplete histone-to-protamine exchange and infertility in mice. In: PLoS Genet 18 (6), e1010272. DOI: 10.1371/journal.pgen.1010272.
2. Braegelmann, C.; Niebel, D.; Ferring-Schmitt, S.; Fetter, T.; Landsberg, J.; Hölzel, M. et al. (2022): Epigallocatechin-3-gallate exhibits anti-inflammatory effects in a human interface dermatitis model-implications for therapy. In: Journal of the European Academy of Dermatology and Venereology : JEADV 36 (1), S. 144–153. DOI: 10.1111/jdv.17710.
3. Esser, Laura Kristin; Branchi, Vittorio; Shakeri, Farhad; Simon, Adrian Georg; Stephan, Carsten; Kristiansen, Glen et al. (2022): Overexpression of Parkin in clear cell renal cell carcinoma decreases tumor aggressiveness by regulating CKS2 levels. In: International journal of oncology 60 (2). DOI: 10.3892/ijo.2022.5310.
4. Funke, Kai; Düster, Robert; Wilson, Prince De-Graft; Arévalo, Lena; Geyer, Matthias; Schorle, Hubert (2022): Transcriptional CDK Inhibitors as Potential Treatment Option for Testicular Germ Cell Tumors. In: Cancers 14 (7). DOI: 10.3390/cancers14071690.
5. Hauke, Jan; Harter, Philipp; Ernst, Corinna; Burges, Alexander; Schmidt, Sandra; Reuss, Alexander et al. (2022): Sensitivity and specificity of loss of heterozygosity analysis for the classification of rare germline variants in BRCA1/2: results of the observational AGO-TR1 study (NCT02222883). In: Journal of Medical Genetics 59 (3), S. 248–252. DOI: 10.1136/jmedgenet-2020-107353.
6. Karagiannis, Fotios; Peukert, Konrad; Surace, Laura; Michla, Marcel; Nikolka, Fabian; Fox, Mario et al. (2022): Impaired ketogenesis ties metabolism to T cell dysfunction in COVID-19. In: Nature 609 (7928), S. 801–807. DOI: 10.1038/s41586-022-05128-8.
7. Leven, Patrick; Schneider, Reiner; Siemens, Kevin D.; Jackson, Walker S.; Wehner, Sven (2022): Application of a RiboTag-based approach to generate and analyze mRNA from enteric neural cells. In: Neurogastroenterology and motility 34 (7), e14309. DOI: 10.1111/nmo.14309.
8. Mallesh, Shilpashree; Hove, Anne S. ten; Schneider, Reiner; Schneiker, Bianca; Efferz, Patrik; Kalff, Jörg C. et al. (2022): Sympathetic Innervation Modulates Mucosal Immune Homeostasis and Epithelial Host Defense. In: Cells 11 (16). DOI: 10.3390/cells11162606.
9. Merges, Gina Esther; Meier, Julia; Schneider, Simon; Kruse, Alexander; Fröbius, Andreas Christian; Kirfel, Gregor et al. (2022): Loss of Prm1 leads to defective chromatin protamination, impaired PRM2 processing, reduced sperm motility and subfertility in male mice. In: Development (Cambridge, England) 149 (12). DOI: 10.1242/dev.200330.
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11. Schneider, Reiner; Leven, Patrick; Mallesh, Shilpashree; Breßer, Mona; Schneider, Linda; Mazzotta, Elvio et al. (2022): IL-1-dependent enteric gliosis guides intestinal inflammation and dysmotility and modulates macrophage function. In: Commun Biol 5 (1), S. 811. DOI: 10.1038/s42003-022-03772-4.
12. Vennin, Constance; Hewel, Charlotte; Todorov, Hristo; Wendelmuth, Marlon; Radyushkin, Konstantin; Heimbach, André et al. (2022): A Resilience Related Glial-Neurovascular Network Is Transcriptionally Activated after Chronic Social Defeat in Male Mice. In: Cells 11 (21). DOI: 10.3390/cells11213405.
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14. Zillich, Lea; Poisel, Eric; Frank, Josef; Foo, Jerome C.; Friske, Marion M.; Streit, Fabian et al. (2022): Multi-omics signatures of alcohol use disorder in the dorsal and ventral striatum. In: Translational Psychiatry 12 (1), S. 190. DOI: 10.1038/s41398-022-01959-1.


Acknowledgements
Administration Medical Faculty
Documents
The Core Facilities thank the German Research Foundation for continuous support.
