A hydrogel beads based platform for single-cell phenotypic analysis and digital molecular detection

Abstract

Microfluidic platforms integrating phenotyping and genotyping approaches have the 19 potential to advance the understanding of single cell genotype-to-phenotype correlations. These 20 correlations can play a key role in tackling antibiotic heteroresistance, cancer cell heterogeneity, 21 and other related fundamental problems. Herein, we report a novel platform that enables both high-22throughput digital molecular detection and single-cell phenotypic analysis, utilizing nanoliter-23 sized biocompatible polyethylene glycol hydrogel beads produced by a convenient and disposable 24 centrifugal droplet generation device. The hydrogel beads have been demonstrated enhanced 25 thermal stability, and achieved uncompromised efficiencies in digital polymerase chain reaction, 26 digital loop-mediated isothermal amplification, and single cell phenotyping. The crosslinked 27 hydrogel network highlights the prospective linkage of various subsequent molecular analyses to 28 address the genotypic differences between cellular subpopulations exhibiting distinct phenotypes. 29Our platform shows great potential for applications in clinical practice and medical research, and 30 promises new perspectives in mechanism elucidation of environment-evolution interaction and 31 other basic research areas. 32