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Related Experiment Video

Updated: Apr 11, 2026

Transcriptome Analysis of Single Cells
07:27

Transcriptome Analysis of Single Cells

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Capture and enumeration of mRNA transcripts from single cells using a microfluidic device.

Matthew T Walsh1, Alexander P Hsiao, Ho Suk Lee

  • 1Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. x2huang@ucsd.edu.

Lab on a Chip
|June 5, 2015
PubMed
Summary

We developed a microfluidic device for automatic single mammalian cell capture and digital counting of polyadenylated mRNA. This technology enables single-molecule sensitivity for RNA transcript enumeration in individual cells.

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Last Updated: Apr 11, 2026

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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons
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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

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Area of Science:

  • Molecular Biology
  • Biotechnology
  • Microfluidics

Background:

  • Accurate RNA transcript measurement is crucial for cell type classification and understanding cellular heterogeneity in health and disease.
  • Existing methods face challenges in precise quantification at the single-cell level.

Purpose of the Study:

  • To develop a microfluidic device for automatic hydrodynamic capture and digital counting of polyadenylated mRNA from single mammalian cells.
  • To enable single-molecule sensitivity for RNA transcript enumeration.

Main Methods:

  • Development of a microfluidic device for hydrodynamic cell capture.
  • Immobilization of single cells and release of polyadenylated mRNA.
  • Single-molecule fluorescence imaging for digital counting of mRNA molecules using surface-attached oligonucleotides.

Main Results:

  • Demonstrated capture of polyadenylated mRNA from single HeLa cells within minutes.
  • Observed significant variation in total mRNA molecule counts among individual cells.
  • Achieved single-molecule sensitivity in RNA transcript counting.

Conclusions:

  • The developed microfluidic technology allows for direct digital enumeration of RNA transcripts from single cells.
  • This approach provides a powerful tool for characterizing cellular heterogeneity.
  • Opens possibilities for precise cell classification and disease research.