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FACS Core Facility

Flow Cytometry Core Facility at the “Centre for Infection Medicine” 

The FACS Core Facility (FCF) offers all scientists of the Freie Universität Berlin access to established and innovative methods of cell analyses and sorting according to their specific needs and interests.

  • BD FACSAria III cell sorter
  • BD FACSCanto II analyser
Laser and filter combinations: Equipment
  • Analyses and sorting of cells from different species, organs and compartments
    (e.g. mouse, human, pig, dog; lymphatic organs, gut, skin, blood, epithelia)
  • Analyses and sorting of cell lines, infected cells, transfected cells/organisms
    (e. g. lymphocytes, cell lines, transfected cells)
  • Sorting of infectious material (S2); requests for the sorting of material potentially harmful to the staff may be rejected


Our service includes:

  • Operator-based cell sorting
  • Independent sample acquisition and analyses

Our cell analyzer BD FACS Canto II is equipped with 3 lasers (405, 488 and 632 nm) and our cell sorter FACS ARIA III with 4 lasers (405 nm, 488 nm, 561 nm und 632 nm).



service fee / h

Analyser (Canto II)

25 €

Sorter (Aria III)

70 € (incl. operator)

Currently the service of the FCCF is only available to members of the Freie Universität Berlin.
Booking is possible up to 14 days in advance. The devices can be booked via the OpenIRIS booking system of the Freie Universität Berlin:


Bookings can’t be changed/deleted on the booked day. The devices can’t be booked on weekends and Berlin holidays. Bookings have to be deleted at least 24 h in advance or a 2 h booking fee will be charged.

For more information about the booking process via OpenIRIS you can download a handout here.

Preliminary talk

Before sorting of samples the aims and conditions have to be clarified with the operator. In case of standard sort procedures (human or mouse samples, standard dyes) this can be done via E-mail/telephone. The estimate sorting time and adjust the sorter set-up, the operator needs information on cell type (size, origin, infectious material), cell numbers (total, target cells), used fluorochromes and subsequent cell use (in vitro cultures, mRNA isolation etc.).

Samples for cell sorting have to be prepared properly:  

  • cell suspensions have to be filtered before sorting (40µm cell strainers).
  • The sample buffer has to be free of phenol red.
  • Samples treated with prodium iodide or DAPI are not accepted for sorting.
  • The operator has to be informed in case other potentially leaky dyes are present in the samples.
  • Unstained negative controls and fluorescence minus one controls (FMOC, in case of extensive fluorochrome panels and dim signals of target cell markers) may be helpful for setting up the sorting strategy.


The FCF staff offers help in preparing sorting strategies and fluorochrome panels.

Cell sorting is performed by the FCF operators within their duty hours and only possible after booking in OpenIRIS.


The analyser may be used independently after an introduction by the FCF.

The data are best directly saved on the server of the respective institute. Alternatively, data may be saved on the server of the institute and then transferred to portable devices.

External storage media must not be used on the computers connected to the sorter/analyser!

Data have to be deleted directly after export from the computers connected to the sorter/analyser.

Data are not permanently stored by the FCF.