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Related Concept Videos

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells
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SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing.

Jinzhou Yuan1, Jenny Sheng2, Peter A Sims3,4,5

  • 1Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.

Genome Biology
|December 26, 2018
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SCOPE-Seq links live cell imaging with single-cell RNA sequencing using optically decodable beads and microfluidics. This innovation enables accurate phenotypic analysis alongside gene expression profiling for comprehensive biological insights.

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Area of Science:

  • Biotechnology
  • Genomics
  • Cell Biology

Background:

  • Optically decodable beads provide sample identification for various biological measurements.
  • This technology underpins microarray, sequencing, and flow-based expression profiling.
  • Linking cellular phenotype to genetic data is crucial for understanding biological systems.

Purpose of the Study:

  • To develop a method combining live cell imaging with single-cell RNA sequencing.
  • To demonstrate the accuracy and scalability of this novel approach.
  • To introduce Single Cell Optical Phenotyping and Expression sequencing (SCOPE-Seq).

Main Methods:

  • Integration of microfluidics with optically decodable beads.
  • Development of the SCOPE-Seq platform.
  • Application to phenotypic analysis and gene expression profiling of single cells.

Main Results:

  • Successful linkage of phenotypic analysis of living cells to single-cell sequencing.
  • Demonstration of the accuracy of the SCOPE-Seq method.
  • Proof-of-concept for the scalability of SCOPE-Seq.

Conclusions:

  • SCOPE-Seq accurately combines live cell imaging with single-cell RNA sequencing.
  • The platform is scalable for comprehensive biological analysis.
  • This integrated approach advances the study of cellular phenotypes and gene expression.