Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics: An Engineering Head Start
AuthorsConchouso Gonzalez, David
KAUST DepartmentElectrical and Computer Engineering Program
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
Biological and Environmental Science and Engineering (BESE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/669662
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AbstractDroplet microfluidic techniques have shown promising results to study single cells at high throughput. However, their adoption in laboratories studying "-omics" sciences is still irrelevant because of the field's complex and multidisciplinary nature. To facilitate their use, here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput. First, a device encapsulating single cells in droplets at a rate of ∼ 250 Hz is described considering droplet size and cell growth. Then, we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers (i.e., 405, 488, 561, and 637 nm) in a single platform to make it compatible with different fluorescence-emitting biosensors. For this sorter, both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz. Then, a passive droplet merger is also integrated into our method to enable adding new reagents to already-made droplets at a rate of 200 Hz. Finally, we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools. Because of the overall integration and the technical details presented here, our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability (> 50,000 cells/day) to mining and bioprospecting metagenomic data.
CitationConchouso, D., Al-Ma’abadi, A., Behzad, H., Alarawi, M., Hosokawa, M., Nishikawa, Y., … Gojobori, T. (2021). Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics: An Engineering Head Start. Genomics, Proteomics & Bioinformatics. doi:10.1016/j.gpb.2021.03.010
SponsorsThe work was supported by the grants from King Abdullah University of Science and Technology (KAUST), Saudi Arabia (Grant Nos. BAS/1/1059/01/01, URF/1/1976/03/01, URF/1/1976-17-01, URF/1/1976-20-01, and FCS/1/3326-01-01). Finally, we thank the nanofabrication and the microfluidics Core Laboratories at KAUST for their support in realizing these microfluidic technologies.
Except where otherwise noted, this item's license is described as This is an open access article under the CC BY license.
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