Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding

Nat Biotechnol. 2017 Jul;35(7):640-646. doi: 10.1038/nbt.3880. Epub 2017 May 29.


The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations.

Publication types

  • Evaluation Study

MeSH terms

  • Cell Separation / instrumentation
  • Chromosome Mapping / instrumentation*
  • DNA Barcoding, Taxonomic / instrumentation*
  • Equipment Design
  • Equipment Failure Analysis
  • Genome / genetics*
  • High-Throughput Nucleotide Sequencing / instrumentation*
  • Lab-On-A-Chip Devices*
  • Tissue Array Analysis / instrumentation*