Project Z02
Treg commons
In the TRR 355, several labs across the partner sites in Munich and Mainz as well as in affiliated institutes investigate aspects of Treg cells in different tissue microenvironments. To do so, many projects rely on the isolation and characterization of lymphoid and non-lymphoid Treg cells and plan to use state of-the-art sequencing-based analytical methods such as single-cell chromatin accessibility mapping, single-cell gene expression analysis, or characterization of T cell receptor expression landscape of tissue-derived T cells. In addition, novel amendments to existing technologies (e.g., barcoding of different samples, quantitative surface protein analysis using barcode-labeled antibodies) or entirely new technologies (e.g. physical cell interaction of cells, combined scATAC/RNA/TCR-Seq, spatial transcriptomics and epigenomics) require careful optimization of both wet-lab protocols and associated bioinformatics.
Z02, as a central project for all research groups of this consortium, will collect, optimize, and validate protocols to generate sequencing-based datasets of tissue Treg cells.
This will include wet-lab protocols to isolate and pre-enrich Treg cells from different murine and human tissues, single-cell processing guides to generate gene expression, chromatin accessibility, or T cell receptor (TCR) sequencing libraries using equipment available at the respective sites, and library preparation plus sequencing guidelines. In addition to wet-lab protocols, Z02 will adapt and provide optimized bioinformatic analysis workflows for datasets generated using these protocols, which will include a centralized storage platform with high-performance computational capacity, a user-friendly interface to select and process the data, and a tool for the generation of output files for data visualization and further analysis.
The flow chart illustrates data flow (blue) and personal communication (green) in the Treg commons platform. The platform will be hosted on the recently-installed (2023) high-performance computing cluster MOGON NHR south-west, a system operating with 590 nodes, 75.000 central processing units, 186 terabytes of RAM and more than 8.000 terabytes of storage capacity. This will ensure sufficient processing power and storage for the Treg commons platform.
In close collaboration with the IRTG, Z02 will teach both wet-lab and bioinformatics to interested technicians, PhD students, and scientists in the consortium. The combination of protocol standardization and optimization with bioinformatics workflows and data visualization in the Treg commons platform will increase the comparability of datasets across labs to strengthen collaboration, reduce the overall experimental cost, analysis time and animal numbers, and provide the opportunity for a comparison of datasets across labs and institutes to address scientific questions, such as: what is the influence of species (mouse vs human), health status or microbiota on Treg cell architecture in different microenvironments? Which signaling pathways or metabolic parameters are affected by these changes?