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Related Experiment Video

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High Throughput Single-cell and Multiple-cell Micro-encapsulation
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Deterministic Co-encapsulation of Microparticles in Droplets via Synchronized Merging for Single-Cell Genomics.

Yanan Du1, Chuhe Wen1, Yuan Luo2

  • 1School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Analytical Chemistry
|November 19, 2025
PubMed
Summary

This study introduces a novel droplet encapsulation method for precisely co-encapsulating multiple microparticles. This technique enhances high-throughput bioanalytical assays, including single-cell genomics, by enabling user-defined ratios.

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Area of Science:

  • Biotechnology
  • Microfluidics
  • Genomics

Background:

  • Droplet encapsulation is crucial for high-throughput bioanalytical assays like single-cell genomics.
  • Precisely co-encapsulating multiple microparticles at defined ratios presents a significant technical challenge.

Purpose of the Study:

  • To develop a robust strategy for deterministic co-encapsulation of microparticles at user-defined ratios.
  • To enable efficient particle pairing for advanced bioanalytical applications.

Main Methods:

  • A novel method combining particle-triggered droplet generation with synchronized droplet merging in a microfluidic channel.
  • Systematic characterization of hydrogel particle co-encapsulation at various sizes and ratios (55 and 80 μm at 1:1 and 2:1).

Main Results:

  • Demonstrated reliable co-loading of hydrogel particles at specified ratios.
  • Developed a single-cell 16S rRNA gene sequencing workflow using co-encapsulated hydrogel capsules and barcode beads.
  • Achieved accurate, high-throughput single-cell taxonomic profiling of microbial mixtures (E. coli and B. subtilis).

Conclusions:

  • The developed deterministic co-encapsulation strategy offers a simple and robust solution for precise microparticle loading.
  • This approach has broad applicability in single-cell genomics, digital assays, and interaction studies requiring controlled particle pairing.