The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding
Open accessAbstract
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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Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
Klein, A. M., Mazutis, L., Akartuna, I., Tallapragada, N., Veres, A., Li, V., Peshkin, L., Weitz, D. A., & Kirschner, M. W. (2015) · Cell · doi:10.1016/j.cell.2015.04.044 · Cited by 3,356
Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state
Rotem, A., Ram, O., Shoresh, N., Sperling, R. A., Goren, A., Weitz, D. A., & Bernstein, B. E. (2015) · Nature Biotechnology · doi:10.1038/nbt.3383 · Cited by 854
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Gole, J., Gore, A., Richards, A., Chiu, Y.-J., Fung, H.-L., Bushman, D., Chiang, H.-I., Chun, J., Lo, Y.-H., & Zhang, K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2720 · Cited by 238
Cited by
Gut microbiota in colorectal cancer development and therapy
Wong, C. C., & Yu, J. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00766-x · Cited by 721
Recent Advances in Droplet Microfluidics
Ding, Y., Howes, P. D., & deMello, A. J. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b05047 · Cited by 357
High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
Zheng, W., Zhao, S., Yin, Y., Zhang, H., Needham, D. M., Evans, E. D., Dai, C. L., Lu, P. J., Alm, E. J., & Weitz, D. A. (2022) · Science · doi:10.1126/science.abm1483 · Cited by 283
“By contrast, lysing,whole-genomeamplification, and labeling of bacterial DNA require multiple microfluidic steps; consequently, although each of these steps has been performed individually in droplets they have not thus far been combined into a unified droplet-based workflow that takes in bacteria and outputs whole ge…”
BackgroundMethodGenomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Munk, P., Brinch, C., Møller, F. D., Petersen, T. N., Hendriksen, R. S., Seyfarth, A. M., Kjeldgaard, J. S., Svendsen, C. A., van Bunnik, B., Berglund, F., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34312-7 · Cited by 304
Development and future of droplet microfluidics
Nan, L., Zhang, H., Weitz, D. A., & Shum, H. C. (2024) · Lab on a Chip · doi:10.1039/d3lc00729d · Cited by 253
Metadata
- Authors
- Lan, F., Demaree, B., Ahmed, N., & Abate, A. R.
- Venue
- Nature Biotechnology
- Published
- 2017-05-29
- Volume
- 35
- Issue
- 7
- Pages
- 640-646
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2620147451
- Cited by
- 431
- References
- 5
- FWCI
- 18.86
- Type
- journal article
- Language
- en
- Open access
- green
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