Interfacing picoliter droplet microfluidics with addressable microliter compartments using fluorescence activated cell sorting

•The addition of low gelling point agarose to microfluidic picoliter scale droplets allowed droplets to be transferred to an aqueous buffer while retaining cell (eGFP expressing Escherichia coli) compartmentalization.•Fluorescence activated cell sorting (FACS) and agarose gelation provides a means to interface picoliter scale droplet microfluidics with a macro scale 672 well slide on a microscope slide footprint.•The combination of small bead size (15 μm diameter), a 100 μm FACS nozzle and a temperature control (4 °C) were key factors for accurate delivery beads into the microwells.•The sorting and delivery of cell containing beads is highly precise: 95% of sorted FACS-drops contain single beads and 97.9% of the sorted beads are accurately placed within the defined well area.•E. coli are found to grow into colonies either outside beads or within beads after 5 h, demonstrating the functionality of the technique for downstream single cell processing and analysis.

Droplet microfluidic platforms have, while enabling high-throughput manipulations and the assaying of single cell scale compartments, been lacking interfacing to allow macro scale access to the output from droplet microfluidic operations. Here, we present a simple and high-throughput method for individually directing cell containing droplets to an addressable and macro scale accessible microwell slide for downstream analysis. Picoliter aqueous droplets containing low gelling point agarose and eGFP expressing Escherichia coli (E. coli) are created in a microfluidic device, solidified to agarose beads and transferred into an aqueous buffer. A Fluorescence activated cell sorter (FACS) is used to sort agarose beads containing cells into microwells in which the growth and expansion of cell colonies is monitored. We demonstrate fast sorting and high accuracy positioning of sorted 15 μm gelled droplet agarose beads into microwells (14 × 48) on a 25 mm × 75 mm microscope slide format using a FACS with a 100 μm nozzle and an xy-stage. The interfacing method presented here enables the products of high-throughput or single cell scale droplet microfluidics assays to be output to a wide range of microtiter plate formats familiar to biological researchers lowering the barriers for utilization of these microfluidic platforms.