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SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing

Yuan, Jinzhou; Sheng, Jenny; Sims, Peter A.

Optically decodable beads link the identity of a sample to a measurement through an optical barcode, enabling libraries of biomolecules to be captured on beads in solution and decoded by fluorescence. This approach has been foundational to microarray, sequencing, and flow-based expression profiling technologies. We combine microfluidics with optically decodable beads and show that phenotypic analysis of living cells can be linked to single-cell sequencing. As a proof-of-concept, we demonstrate the accuracy and scalability of our tool called Single Cell Optical Phenotyping and Expression sequencing (SCOPE-Seq) to combine live cell imaging with single-cell RNA sequencing.

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Single-cell RNA-Seq, Live cell imaging, Microfluidics