Technology and Analytics for Sequencing Physically Interacting Cells

This project will develop the technology and analytics to sequence pairs of attached tissue cells to determine their interactions and spatial localization. The network will apply these approaches to reconstruct 3D maps and interaction models in the human intestine and bone marrow, studying how cell interactions impact differentiation, proliferation, metabolism, and more.

Developing protocols and technologies for tissue dissociation was critical for this project. To enable the enrichment of physically interacting cells without the use of surface markers, they developed a technique for a chemical-based tissue dissociation protocol and coupled this with Hoescht cell sorting. To analyze data generated using this protocol, they created a deconvolution algorithm called ClumpSeq to classify cell “clumps.” Together, these tools provide a framework to identify physically interacting cell pairs.