Virtual microfluidics for digital quantification and single-cell sequencing

Liyi Xu; Ilana L Brito; Eric J Alm; Paul C Blainey

doi:10.1038/nmeth.3955

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.

Authors

Liyi Xu^{1

2}, Ilana L Brito^{1

2

3}, Eric J Alm^{1

2

3}, Paul C Blainey^{1

2}

Affiliations

¹ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
² The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
³ The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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.

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

Substances

Hydrogels

Abstract

MeSH terms

Substances

Grants and funding