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Improving single-cell transcriptome sequencing efficiency with a microfluidic phase-switch device.

Authors
  • Zhang, Baoyue1
  • Xu, Hong
  • Huang, Yuqing
  • Shu, Weiliang
  • Feng, Hongtao
  • Cai, Jin
  • Zhong, Jiang F
  • Chen, Yan
  • 1 Key Lab for Health Informatics of Chinese Academy of Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. [email protected] , (China)
Type
Published Article
Journal
The Analyst
Publisher
The Royal Society of Chemistry
Publication Date
Dec 02, 2019
Volume
144
Issue
24
Pages
7185–7191
Identifiers
DOI: 10.1039/c9an00823c
PMID: 31688860
Source
Medline
Language
English
License
Unknown

Abstract

In this paper, we present a novel method to improve the efficiency of single-cell transcriptome sequencing for analyzing valuable cell samples. The microfluidic device we designed integrates multiple single-cell isolation chambers with hydrodynamic traps and achieves a nearly 100% single-cell capture rate and minimal cell loss, making it particularly suitable for samples with limited numbers of cells. Single cells were encapsulated using a novel phase-switch method into picoliter-sized hydrogel droplets and easily recovered for subsequent reactions. Minimizing the reaction volume resulted in a high reverse transcription (RT) efficiency for RNA sequencing (RNA-Seq). With this novel microfluidic platform, we captured dozens of hESCs (H9) simultaneously and obtained live cells in individual picoliter volumes, thus allowing for the convenient construction of a high-quality library for deep single-cell RNA-Seq. Our single-cell RNA-Seq results confirmed that a spectrum of pluripotency existed within an H9 colony. This integrated microfluidic platform can be applied to various cell types for the investigation of rare cellular events, and the phase-switch single-cell processing strategy will improve the efficiency and accessibility of single-cell transcriptome sequencing analysis.

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