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Genome Biol. 2018 Dec 24;19(1):227. doi: 10.1186/s13059-018-1607-x.

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

Author information

1
Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
2
Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, 10032, USA.
3
Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA. pas2182@columbia.edu.
4
Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA. pas2182@columbia.edu.
5
Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, 10032, USA. pas2182@columbia.edu.

Abstract

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.

KEYWORDS:

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

PMID:
30583733
PMCID:
PMC6305572
DOI:
10.1186/s13059-018-1607-x
[Indexed for MEDLINE]
Free PMC Article

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