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

Nature Biotechnology volume 35, pages 640646 (2017) | Download Citation

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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.

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  • 21 June 2017

    In the version of this article initially published, in Figure 3c, bars on the x axis were labeled S. epidermidis rather than S. enterica. The error has been corrected for the print, PDF and HTML versions of this article.


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We are grateful for K. Stedman, R. Malmstrom, R. Andino, K. Pollard, and M. Fischbach for very helpful discussion of and advice on the manuscript. We thank C. O'Loughlin at UCSF for providing microbial strains. This work was supported by the National Science Foundation through a CAREER Award (grant number DBI-1253293); the National Institutes of Health (NIH) (grant numbers HG007233-01, R01-EB019453-01, 1R21HG007233, DP2-AR068129-01, R01-HG008978); and the Defense Advanced Research Projects Agency Living Foundries Program (contract numbers HR0011-12-C-0065, N66001-12-C-4211, HR0011-12-C-0066). Funding for open access charge: (NIH grant number DP2-AR068129-01). F.L. is supported by a PGS-D grant from the National Science and Engineering Research Council of Canada (NSERC).

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    • Adam R Abate

    Present address: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.


  1. Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, California, USA.

    • Freeman Lan
    • , Benjamin Demaree
    • , Noorsher Ahmed
    •  & Adam R Abate
  2. UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, California, USA.

    • Freeman Lan
    • , Benjamin Demaree
    •  & Adam R Abate
  3. Chan Zuckerberg Biohub, San Francisco, California, USA.

    • Adam R Abate


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F.L. and A.R.A. conceived of the SiC-seq method. F.L., B.D., and N.A. designed and performed the experiments, and analyzed data. F.L. and A.R.A. wrote the manuscript.

Competing interests

Patents pertaining to this workflow may be licensed to Mission Bio, of which A.R.A. is a shareholder.

Corresponding author

Correspondence to Adam R Abate.

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