Automated preparation of single-cells and nuclei from solid tissues

Project Summary AbstractThis project designsdevelopsand automates a novel system to process solid tissue into single cellssingle nucleiand high molecular weight DNA using disposable cartridges without user interventionThe system will support downstream single cell RNA or DNA sequencingsingle nuclei RNA or DNA sequencingand long read sequencers and optical mappingThe long term goal of the project is to enable researchers and clinicians with sample to answer solutions for fully integrated sequencing of solid tissues including biopsy samplesIn the Phase I projectautomated workflows are developed and optimized in novelfully integrated cartridge designsThe prototype system is first benchmarked against an Sbreadboard system and manual processes for single cell production from mouse tissuesCartridgesmechanical disruptionenzymologyand workflows are further developed and optimized for mouse and rat tissues for fully integrated processing performanceA cartridge formg tissue specimens is designed and testedProcessing single cells into high molecular weight DNA is tested using the magnetic separations in the cartridge and on other devicesThe automated preparation of nuclei will be tested and developed on prototype systemsSingle cell suspensions prepared on the prototype will be processed into nuclei by chemical lysis in the cartridge and magnetic purification of nuclei with paramagnetic beads testedEnzymatic formulations with gentler processing will be studiedWorkflows and cartridges to directly process tissue into nuclei will be developed and testedThe single sample prototype systems will be tested externally at the J Craig Venter Institute and the Broad InstitutePhase I testing will design the architecture of a multi sample preproduction prototype system with additional capabilities to be built and tested in Phase IIAn optical module will be added to determine viability and titer on the system and potentially allow the system to adjust dissociation protocolson the flyIntegrated magnetic processing will be further developed to purify cell typesnuclei and other organellesand DNAThe project output will bea validated single sample tissue to cellnucleior high molecularweight DNA automated prototypeanda multiple sample design architected for Phase II development Project NarrativeThis project develops a system to automatically process solid tissues into single cellsnucleiand high molecular weight DNAThe system addresses the pipeline gap of preparing cells and nuclei from tissue for single cell next generation sequencingNGSThe system will allow the full power and scale of NGS to be applied to primary solid tissue samples and will help standardize research and clinical applications of single cells and nucleiMore broadlythe system will help create a fully integrated tissue to answer sequencing system in the future