Collaborative Project

Lymphatic tissue and in situ transcriptomic profiling

This collaboration of a Tissue Mapping Center (TMC) at the University of Florida (UF) and a Transformative Technology Development group (TTD) at Cal Tech aims to collect high-content, spatially resolved transcriptomic data in lymphatic tissue types, apply this data to feed back on the protein analysis in each tissue and build a 3D map of each tissue at protein and transcript level detail.

The lymphatic system is distributed throughout the body, both in the blood and within secondary organs such as the lymph nodes, spleen and thymus, where they serve surveillance functions for the immune system. Protein localization technologies, which detect the presence of specific proteins, and transcriptomic profiling technologies, which profile the presence of messenger RNA (mRNA) that the cell uses to translate genes into functional proteins, offer complementary strengths in visualizing the locations, types and activities of lymphatic cells in each locale.

In this collaboration, the UF TMC provides preserved lymph node, spleen and thymus samples to the Cal Tech TTD, in an iterative process to optimize experimental conditions and techniques. All data will be transferred to the HIVE and accessible by HuBMAP Consortium members. To date, the probe set has been expanded from an initial 50 to approximately 400 genes relevant to lymph node and thymus function. In addition, UF provides fresh tissue to Cal Tech for seqFISH (direct imaging of mRNA with a complementary fluorescent-labeled DNA probe) on tissues to investigate improvements in preservation based on the collaboration’s prior experience.

Project Leads
Long Cai, Cal Tech TTD

Learn more about Cal Tech TTD.

Clive Wasserfall, University of Florida TMC

Learn more about University of Florida TMC.


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