title: Virtual microfluidics for digital quantification and single-cell sequencing.
abstract: 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.
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Liyi
authors.initials: L
authors.lastname: Xu
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Ilana L
authors.initials: IL
authors.lastname: Brito
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Blainey
mesh_terms: D059018:DNA Contamination; D001330:Electronic Data Processing; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020100:Hydrogels / Q000737:chemistry; D044085:Microfluidics / Q000379:methods*; D008856:Microscopy, Fluorescence; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D013211:Staphylococcus aureus / Q000235:genetics; D014584:User-Computer Interface; D057188:Workflow
chemical_list: D020100:Hydrogels