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

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