Abstract

The motivation to engineer biological systems through standardization and abstraction sparked the development of technological advances in automation of life sciences since the early 2000’s. Now, robotics are performing high-throughput tasks with increasingly higher precision and control over the environment of precious biological samples. At the same time, a different set of hardware has emerged in the life-sciences: while robotics enable for high-throughput automation, microfluidics - the discipline of handling fluids on a micro scale - allows researchers and clinicians to perform experiments they could not have imagined before. These highly controlled devices can purify proteins, engineer cells, gain insights to single-cell ‘omic’ information, or filter out a patient’s cancer cells in a fully automated fashion. In this work, we are focused on designing novel microfluidic devices for single-cell analysis. Currently, the use of single-cell analysis microfluidic devices open up the possibility of gaining detailed insights in heterozygosity of cell populations when coupled with next-generation sequencing technologies. We propose the design of a microfluidic setup that has improved control over single-cell operations within droplet-in-channel microfluidic architectures compared to current systems. Expanding these ’droplet digital’ tools, we have developed a microfluidic system for binary sorting of droplet libraries, on-demand droplet generation, droplet mixing, droplet storage and release, and deterministic encapsulation of single-cells . We propose new methods to sort cells, such as filamentous fungi libraries based on enzyme production, yeast based on growth rate and mammalian cell single-clones based on gene-editing efficiency. This work involves the development of novel hardware and software, and the integration of our microfluidic device within an automation system to operate dropletdigital microfluidics. Such systems are expanding the toolbox of those who are ‘engineering biology’.