Single Cell Technologies


Molecular, biochemical and functional analyses at the population level always represent the average result of all input cells, ignoring cellular heterogeneity. To overcome these obstacles, the unit provides both established as well as novel single cell technologies that facilitate quantitative measurements of gene and protein expression linked to cell fate and functional analyses at the single cell level.


  • Multiparameter flow cytometry (16-colour-FACS devices): Cell analyses and cell sorting of viable primary cells using complex combinations of extracellular and intracellular staining. Single cell deposition via FACS sorting in individual wells (also for index sorting). Several 8-marker panels for immune profiling for clinical studies and assays to quantify cell function and fate, cell signaling (Phosphoflow) and gene expression.
  • PrimeFlow RNA expression by flow cytometry to quantitatively measure multiplex RNA expression (mRNA, IncRNA, miRNA) at the single cell level in heterogeneous populations and to quantify protein and mRNA pairs simultaneously at high throughput and single cell resolution.
  • Time-lapse microscopy-based single cell tracking for continuous observation of individual cells and their progeny at high spatial and temporal resolution; allows for tracking of single cell behavior, fate and function in real-time. Up to five different fluorescent signals can be detected. Cells can be observed with our unique technology for weeks without losing cell identity. Statistic analysis of generated cell pedigrees (genealogy) and quantitative fluorescent signal tracking.
  • Multiplex signaling studies in single cells via flow cytometry to measure multiple (up to 5) signaling pathways simultaneously in identical single cells in heterogeneous populations using surface marker co-stainings. 
  • Automated capillary-based Western Blot enables highly sensitive and ultra-fast protein detection after size separation. Only 50 ng of total protein per lane required and fully automated detection in only 4 hours. Titrations down to single cell equivalents possible.
  • Single cell genomics and transcriptomic analyses via Fluidigm C1-based single cell sequencing (RNA, exome, miRNA and ATAC sequencing) 


Head of unit:
Prof. Dr. rer. nat. Michael Rieger
University Hospital Frankfurt
LOEWE Center for Cell and Gene Therapy
Department of Medicine II, Hematology/Oncology

Lena Dorsheimer
Tel.: +49 (0)69/6301-84231