Flow Cytometry Core Facility

The Flow Cytometry Core Facility offers a range of flow cytometric techniques.

The Flow Cytometry Core Facility offers access to high-end FACS analysis and state-of-the-art cell sorting capabilities, actively providing scientists with adaptive setups and dedicated support.



We offer a wide range of flow cytometric techniques, hands-on service, data analysis and tailored training sessions for users from inside and outside EMBL.

Our specialised equipment adds flexibility in the preparation and execution of experiments, allowing tailored approaches to addressing scientific problems.

Our facility strives to meet researchers’ specific needs by providing dedicated help with experimental design, enabling the highest possible resolution in terms of analysis and product. We have recently upgraded the facility to provide access to S2 cell sorting services and improved our general sorting setup to meet the growing need for high-parametric and aseptic sorting.

We work with equipment from Beckman Coulter, Becton Dickinson, Union Biometrica, Coherent Inc. and ThermoFisher. The EMBL Flow Cytometry platform is open to test new technological developments to best serve the needs of the scientific community.

Figure 1: Typical profile of CRISPR-Cas9 genome edited mES cell lines for single cell sorting. The facility provides key services, such as sorting heterogeneous cell populations into homogeneous populations based on fluorescence.

Major projects and accomplishments

  • High-throughput sorting of tissue-specific nuclei from Drosophila melanogaster embryo as a preparative step in the analysis of genome regulatory activity during tissue development.
  • Establishment of clonal cell lines carrying fluorescent protein-tagged genome-edited genes for 4D life cell imaging, and assessment of protein interactions and concentrations during mitosis.
  • Large-scale sorting of protoplasts carrying multiple fluorescence reporter constructs for RNAseq.
  • Single-cell sorting of high efficiencies for single cell quantitative genome, transcriptome, CRISPR/Cas9 genome editing and in vitro studies.
  • Creation of high-parametric S2 cell sorting service with dedicated equipment
  • In-house Flow Cytometry course in cooperation with the German Cancer Research Center (DKFZ) in 2016 and to be repeated yearly.
  • Two Flow Cytometry data analysis workshops at Heidelberg and Monterotondo in 2016.
  • Five-day EMBL Course for Hands-on Flow Cytometry to be held in February 2017.
  • Five-day EMBO Practical Course on cell sorting to be held in November 2017.

Services provided

  • Complex multi-colour analysis of cell populations based on light scatter, fluorescent probes content and light intensities (including polarisation).
  • Full-service sorting of rare populations out of a heterogeneous sample. Cell cloning, particle enrichment and high purity bulk sorts.
  • High-recovery and indexed single-cell sorting for sequencing.
  • Providing scientists with expertise in flow cytometric techniques required in their research projects.
  • Providing our researchers with advice and dedicated training sessions in the use of flow cytometry, instrument operation and post-acquisition data analysis.
  • Developing novel flow cytometric techniques to meet EMBL’s diverse scientific needs.


Flow Cytometry Core Facility
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Tel: +49 6221 387-8341
E-mail: diana.ordonez@embl.de

Reservations, trainings and consultations:
E-mail: fccf-team@embl.de