The FACS Facility provides instrumentation, education and expertise for all your flow cytometry needs. The flow cytometry services include both, multi-parameter analysis and sorting of cell populations based on fluorescence labels and on phenotypic and biochemical properties of the cells.


  • Expertise to help users with experimental design and protocol development
  • Analysis and sorting of cell lines and primary tissue cells from various model organisms
  • User training on the Sony MA900 benchtop cell sorter and the Sony SA3800 spectral analyzer


  • Multi-parameter analysis of cell suspensions (up to 20 parameters with 5 lasers (375, 405, 488, 561, 633nm)
  • Cell cycle analysis
  • Cell viability and apoptosis
  • Analysis of fluorescently labeled cell lines and antibody stainings
  • Spectral analysis on our Sony SA3800 spectral analyzer

Cell sorting:

  • Sterile cell sorting of up to 4 subpopulations simultaneously
  • Sterile bulk and single-cell sorting into multiwell-plates (24, 48, 96 and 384 wells)


  • FacsAria Fusion, cell sorter, Beckton Dickinson, 4 laser lines (375/405, 488, 561 and 633 nm); 4-way sterile cell sorting into tubes or single-cell sorting into multiwell-plates.
  • MA900 benchtop cell sorter, Sony, 4 laser lines (405, 488, 561 and 633 nm); 4-way sterile cell sorting into tubes or single-cell sorting into multiwell plates
  • SA3800 spectral analyzer, Sony, 4 laser lines (405, 488, 561 and 633 nm); automatic sampling from tube rack or multiwell plates


* joint first author # joint corresponding author

Kaushikaram Subramanian✳︎, Heike Petzold✳︎, Benjamin Seelbinder✳︎, Lena Hersemann, Ina Nüsslein, Moritz Kreysing
Optical plasticity of mammalian cells.
J Biophotonics, 14(4) Art. No. e202000457 (2020)
Open Access PDF DOI
Transparency is widespread in nature, ranging from transparent insect wings to ocular tissues that enable you to read this text, and transparent marine vertebrates. And yet, cells and tissue models in biology are usually strongly light scattering and optically opaque, precluding deep optical microscopy. Here we describe the directed evolution of cultured mammalian cells toward increased transparency. We find that mutations greatly diversify the optical phenotype of Chinese Hamster Ovary cells, a cultured mammalian cell line. Furthermore, only three rounds of high-throughput optical selection and competitive growth are required to yield fit cells with greatly improved transparency. Based on 15 monoclonal cell lines derived from this directed evolution experiment, we find that the evolved transparency frequently goes along with a reduction of nuclear granularity and physiological shifts in gene expression profiles. In the future this optical plasticity of mammalian cells may facilitate genetic clearance of living tissues for in vivo microscopy.

Marta Florio, Mareike Albert, Elena Taverna, Takashi Namba, Holger Brandl, Eric Lewitus, Christiane Haffner, Alex Sykes, Fong Kuan Wong, Jula Peters, E. Guhr, Sylvia Klemroth, Kay Prüfer, Janet Kelso, Ronald Naumann, Ina Nüsslein, Andreas Dahl, Robert Lachmann, Svante Pääbo, Wieland B. Huttner
Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion.
Science, 347(6229) 1465-1470 (2015)
Evolutionary expansion of the human neocortex reflects increased amplification of basal progenitors in the subventricular zone, producing more neurons during fetal corticogenesis. In this work, we analyze the transcriptomes of distinct progenitor subpopulations isolated by a cell polarity-based approach from developing mouse and human neocortex. We identify 56 genes preferentially expressed in human apical and basal radial glia that lack mouse orthologs. Among these, ARHGAP11B has the highest degree of radial glia-specific expression. ARHGAP11B arose from partial duplication of ARHGAP11A (which encodes a Rho guanosine triphosphatase-activating protein) on the human lineage after separation from the chimpanzee lineage. Expression of ARHGAP11B in embryonic mouse neocortex promotes basal progenitor generation and self-renewal and can increase cortical plate area and induce gyrification. Hence, ARHGAP11B may have contributed to evolutionary expansion of human neocortex.

Martin Kragl, Kathleen Roensch, Ina Nüsslein, Akira Tazaki, Yuka Taniguchi, Hiroshi Tarui, Tetsutaro Hayashi, Kiyokazu Agata, Elly M. Tanaka
Muscle and connective tissue progenitor populations show distinct Twist1 and Twist3 expression profiles during axolotl limb regeneration.
Dev Biol, 373(1) 196-204 (2013)
Limb regeneration involves re-establishing a limb development program from cells within adult tissues. Identifying molecular handles that provide insight into the relationship between cell differentiation status and cell lineage is an important step to study limb blastema cell formation. Here, using single cell PCR, focusing on newly isolated Twist1 sequences, we molecularly profile axolotl limb blastema cells using several progenitor cell markers. We link their molecular expression profile to their embryonic lineage via cell tracking experiments. We use in situ hybridization to determine the spatial localization and extent of overlap of different markers and cell types. Finally, we show by single cell PCR that the mature axolotl limb harbors a small but significant population of Twist1(+) cells.

Anne Meyer, Alexander Jarosch, Katja Schurig, Ina Nuesslein, Stefan Kißenkötter, Alexander Storch
Fetal mouse mesencephalic NPCs generate dopaminergic neurons from post-mitotic precursors and maintain long-term neural but not dopaminergic potential in vitro.
Brain Res, 1474 8-18 (2012)
Stem cells have one major advantage over primary cells for regenerative therapies in neurodegenerative diseases. They are able to self-renew making sufficient quantities of cells available for transplantation. Embryonic stem cells and fetal neural progenitor cells (NPCs) have been transplanted into models for PD with functional recovery of motor deficits. However, their precise characteristics are still unknown and ideal conditions for their long-term expansion and differentiation into dopamine neurons remain to be explored. Mouse fetal NPCs are commonly grown as characteristic neurospheres, but they also proliferate under monolayer culture conditions. We investigated the proliferative behavior and dopaminergic differentiation capacity of fetal mouse midbrain NPCs derived from E10 to E14 embryos expanded either as neurosphere or monolayer culture. We found similar proliferation capacities in NPCs of all embryonic stages. Neuronal differentiation capacity is higher in neurosphere cultures compared to monolayer NPCs and persists in long-term cultures. We did not find dopaminergic differentiation in long-term expanded mouse NPC types, which is in contrast to rat and human fetal midbrain NPCs. Mouse NPCs generate dopaminergic neurons until up to three weeks in vitro but they do not incorporate BrdU. Quantitative analysis showed that they were not just primary neurons from the isolation process but formed to a great extent in vitro during differentiation suggesting that they are formed by promotion of post-mitotic neuroblasts. A detailed transcription profile reveals de-specification processes during in vitro cultivation, which matches their NPC behavior. We provide the constitutive work for studies using fetal midbrain NPCs of mouse including transplantation studies and transgenic models.

Yoko Arai, Jeremy N. Pulvers, Christiane Haffner, Britta Schilling, Ina Nüsslein, Federico Calegari, Wieland B. Huttner
Neural stem and progenitor cells shorten S-phase on commitment to neuron production.
Nat Commun, 2 Art. No. 154 (2011)
During mammalian cerebral cortex development, the G1-phase of the cell cycle is known to lengthen, but it has been unclear which neural stem and progenitor cells are affected. In this paper, we develop a novel approach to determine cell-cycle parameters in specific classes of neural stem and progenitor cells, identified by molecular markers rather than location. We found that G1 lengthening was associated with the transition from stem cell-like apical progenitors to fate-restricted basal (intermediate) progenitors. Unexpectedly, expanding apical and basal progenitors exhibit a substantially longer S-phase than apical and basal progenitors committed to neuron production. Comparative genome-wide gene expression analysis of expanding versus committed progenitor cells revealed changes in key factors of cell-cycle regulation, DNA replication and repair and chromatin remodelling. Our findings suggest that expanding neural stem and progenitor cells invest more time during S-phase into quality control of replicated DNA than those committed to neuron production.