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

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

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Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, California, USA.
UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, California, USA.
Chan Zuckerberg Biohub, San Francisco, California, USA.


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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