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

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.

Researchers from the Columbia University Irving Medical Center 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.


a Workflow for generating the dual-barcoded beads and the associated bead-free DNA sequencing libraries. b Sequence composition of the bead-bound mRNA capture oligonucleotides and optical barcode oligonucleotides (OBOs). c A look-up table linking sequence barcodes and optical barcodes. d Workflow for SCOPE-Seq. e Workflow for linking live, single-cell imaging data with single-cell RNA-Seq profile

Yuan J, Sheng J, Sims PA. (2018) SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing. Genome Biol 19(1):227. [article]

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