Welcome to the Core Facility Integrated Technology Development

The Core Facility for Integrated Technology Development (CF-ITD) at the Institute of Immunology, University Medical Center Mainz, supports researchers along the entire experimental workflow — from tissue processing and advanced cell sorting to sequencing and bioinformatic data analysis.

We provide:

• Best-practice protocols for the isolation of high-quality immune cells from murine and human tissues for single-cell applications
• Advanced cell sorting strategies on the BD FACS Discover S8 with BD SpectralFX™ and BD CellView™ Image technologies, enabling sort decisions based on cell-cell interactions or morphology alongside an extensive surface marker panel
• Technological integration of sample processing, cell sorting, (single) cell processing, next-generation sequencing and proteomics analysis adapted to sample requirements
• Tailored bioinformatic support, including reproducible workflows, customized scripts, and expert guidance for single-cell sequencing data analysis
• Close interaction with core facility flow cytometry (CFFC), core facility next-generation sequencing (CF-NGS), and core facility proteomics (CFMS)

Our mission is to provide state-of-the-art technologies and expertise that enable researchers to address complex immunological questions with precision, reproducibility, and confidence.

The CF-ITD is headed by Prof. Dr. Michael Delacher and coordinated by Dr. Kathrin Braband, who is your main contact for inquiries.

We have established standardised operating procedures (SOPs) for isolating immune cells from murine and human non-lymphoid tissues, which we will share with you. Beyond ensuring high cell viability, these protocols are specifically optimized to preserve physiological cell–cell interactions, such as those occurring at the immunological synapse. This enables researchers to explore entirely new questions using the BD FACS Discover S8.

In close collaboration with the CFFC, we provide access to the BD FACS Discover S8 sorter, equipped with advanced image-enabled sorting capabilities. The instrument combines 78 detectors across 5 lasers for BD SpectralFX™ technology with 6 dedicated image-enabled detectors on the blue laser for BD CellView™.

This technology enables:

• Highly multiplexed panel design for in-depth characterization of immune cell populations
• Sorting of physically interacting cells, supported by real-time imaging and analysis
• Morphology-based sorting, such as separation of cells by cell cycle stage or subcellular structural features

Following cell sorting, we collaborate closely with the CF-NGS for sample processing and library preparation. A broad spectrum of sequencing platforms and expertise is available, covering scRNA/TCR-seq and scATAC-seq amongst other applications. Proteome and secretome of your cells of interest can be analysed in collaboration with the Core facility for Mass Spectrometry 

Analyzing your own data is exciting—it gives you unique insights and a deeper understanding that you might miss if someone else did the work for you. At the same time, having an experienced guide can make the process more effective and ensure that your analysis is both accurate and meaningful.

Our bioinformatics support includes:

• Robust, validated workflows for scRNA/TCR-seq and scATAC-seq data processing, including alignment, pre-processing and quality control, and downstream analysis
• Tailored analytical strategies adapted to the specific scientific question
• Guidance in applying and interpreting computational methods, supported by customized scripts where needed
• Analysis pipelines established on local high-performance computing infrastructure

This ensures that your data analysis is both scientifically sound and directly relevant to your research objectives.