Virtual microfluidics for digital quantification and single-cell sequencing

Nat Methods. 2016 Sep;13(9):759-62. doi: 10.1038/nmeth.3955. Epub 2016 Aug 1.


We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial cells and human microbiome samples in the virtual microfluidics system, and demonstrated whole-genome sequencing of single-cell MDA products with excellent coverage uniformity and markedly reduced chimerism compared with products of liquid MDA reactions.

MeSH terms

  • DNA Contamination
  • Electronic Data Processing
  • Escherichia coli / genetics
  • Genome, Bacterial*
  • High-Throughput Nucleotide Sequencing / methods*
  • Hydrogels / chemistry
  • Microfluidics / methods*
  • Microscopy, Fluorescence
  • Nucleic Acid Amplification Techniques / methods*
  • Sequence Analysis, DNA / methods*
  • Single-Cell Analysis / methods*
  • Staphylococcus aureus / genetics
  • User-Computer Interface
  • Workflow


  • Hydrogels