CF Functional Genomics

The Core Facility Functional Genomics supports and performs high-throughput image-based experiments combined with RNAi and provides technical expertise and support in high-content analysis microscopy for the quantitative analysis of cellular phenotypes. We also support and perform genome wide pooled screens with our libraries (gRNAs or shRNAs) and assist until hit validation by generating KO/KI cell line(s) for the genes of interest.

Tasks routinely performed by the facility:

Assay Development & Optimization, User training

  • design & optimization of cell-based assays
  • optimization of siRNA transfection
  • high-content analysis (HCA) assay development and optimization
  • assay adaptation to multi-well-plate format
  • work-flow automation
  • statistical analysis
  • user introduction and training
  • organizing workshops


  • high-throughput high-content RNAi screening
  • data analysis
  • hit-picking

Resources and equipment

  • RNAi libraries (sgRNA, shRNA, siRNA)
  • automated high throughput epifluorescence microscope: Thermo Arrayscan VTI
  • automated high throughput spinning disk confocal microscope: MD ImageXPress Micro Confocal
  • liquid handling workstation: Tecan Evo Freedom
  • Cell dispensing device: Biotek CellDispenser
  • Electroporation device: Amaxa 4D-Nucleofector (X and Y units)
  • IT infrastructure for storage & analysis of large datasets in collaboration with SG-IT and CF LSC
  • Pooled CRISPR-CAS9 Screening
    • Wang lab, Biochemistry group
  • Generation of sensor-tested shRNA library

  • Image-based screening
    • Glucocorticoid-induced osteoporosis (collaboration with CME Ulm)
  • High-Content-Analysis (HCA) pipelines
    • Cytospin Images Quantification (Huaibiao Li / Ploubidou Lab)
  • Automated Imaging, HCA-Pipeline and Screening Support
    • Automated cell counting (various labs)
    • Apoptosis and Cell Death assays (various labs)
    • 4Ch Assay (Johannes Jungwirth / Pospiech Group - Englert Lab)
    • Fish embryo transfection screening (Raphael Geissen / Englert Lab)
    • Astrocytes Counting (Gabriela Guerra / Wang Lab)
    • Colony Counting (Annemarie Carlstedt / Morrison Lab)
    • EdU Assay (Morrison Lab)
  • Tissue analysis and quantification
    • Hindbrain Analysis (Christian Hayn / Englert Lab)

Internal users:
Download (pdf) Detailed information on the facility equipment and resources.

External users:
Please inquire.


Torsten Kroll+49 3641 656400eMailCore Facility Manager
Mara Sannai+49 3641 656716eMailResearch Engineer
Sabine Gallert+49 3641 656112eMailTechnical Assistant
Gabriele Günther+49 3641 656306/6752eMailTechnical Assistant
Jana Hamann+49 3641 656052eMailTechnical Assistant
Christoph Kaether+49 3641 656230eMailScientific Supervisor

* incomplete due to Data protection

For publications of individual CF members:  publications search 


Torsten Kroll
CF Manager
+49 3641-656400

Christoph Kaether
Scientific Supervisor

Group Website

Overview CF Functional Genomics