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Related Experiment Video

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Single-cell Gene Expression Profiling Using FACS and qPCR with Internal Standards
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Dean Flow Assisted Single Cell and Bead Encapsulation for High Performance Single Cell Expression Profiling.

Luoquan Li1,2, Ping Wu1,2, Zhaofeng Luo

  • 1BGI-Shenzhen , Shenzhen 518083 , China.

ACS Sensors
|May 4, 2019
PubMed
Summary

This study enhances single-cell expression profiling using droplet microfluidics (Drop-seq) by developing a novel chip that focuses both cells and barcoded beads. This significantly improves cell utilization rates for more efficient single-cell analysis.

Keywords:
Dean flowDrop-seqcell encapsulationinertial microfluidicsscRNA-seqspiral channel

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Area of Science:

  • Biotechnology
  • Genomics
  • Microfluidics

Background:

  • Droplet microfluidics (Drop-seq) is vital for single-cell expression profiling.
  • Traditional Drop-seq faces low efficiency due to challenges in simultaneous single-cell and single-bead encapsulation.
  • Previous methods focused on beads but not cells, limiting potential performance gains.

Purpose of the Study:

  • To design and implement a microfluidic Drop-seq device incorporating spiral and serpentine channels.
  • To focus both barcoded beads and single cells simultaneously within the microfluidic channels.
  • To enhance the efficiency of single-cell encapsulation for expression profiling.

Main Methods:

  • Designed and fabricated a microfluidic chip with integrated spiral and serpentine channels.
  • Implemented the chip within the Drop-seq workflow for single-cell expression profiling.
  • Tested the device by co-encapsulating barcoded beads with human-mouse cell mixtures and subsequent sequencing.

Main Results:

  • Achieved simultaneous focusing of both cells and barcoded beads.
  • Demonstrated a ~300% increase in cell utilization rate compared to traditional Drop-seq.
  • Showed a ~40% improvement in cell utilization rate compared to bead-focusing-only devices.

Conclusions:

  • The novel microfluidic chip design significantly enhances cell utilization in Drop-seq.
  • This approach offers a promising strategy for high-efficiency single-cell expression profiling.
  • The integrated focusing of cells and beads represents a key advancement in microfluidic single-cell analysis.