The CF-ITD offers comprehensive support along the entire experimental workflow—from optimized tissue processing and advanced image-enabled cell sorting to sequencing and tailored bioinformatic analysis. By integrating state-of-the-art technologies with expert guidance, we ensure that each step is conducted with precision, reproducibility, and scientific rigor. Our unique strength lies in guiding researchers through the complete process, enabling them not only to generate high-quality data but also to derive meaningful insights directly aligned with their scientific questions.

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 CFMS.

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.