Journal
NATURE BIOTECHNOLOGY
Volume 35, Issue 7, Pages 640-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt.3880
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Funding
- National Science Foundation [DBI-1253293]
- National Institutes of Health (NIH) [HG007233-01, R01-EB019453-01, 1R21HG007233, DP2-AR068129-01, R01-HG008978]
- Defense Advanced Research Projects Agency Living Foundries Program [HR0011-12-C-0065, N66001-12-C-4211, HR0011-12-C-0066]
- NIH [DP2-AR068129-01]
- PGS-D grant from National Science and Engineering Research Council of Canada (NSERC)
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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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