Automating Your Life Science Workflows

Automation is vital for life scientists looking to improve consistency across samples and runs; it increases throughput, reduces hands-on time, and minimizes errors. 

Figure 1. The Opentrons Flex is a new lab automation platform that is highly modular and able to automate a variety of different life science workflows. Image Credit: Opentrons

However, automation comes with its own set of challenges. Platforms are often either highly customizable, which makes them expensive and complex, or they are user-friendly and affordable but limited to a few specific workflows.

Laboratories require automation that can be custom-built, easy to use, and readily available. This article discusses the automation of the three life science workflows: nucleic acid extraction, NGS library prep, and small-scale protein purification on the new Opentrons Flex.

The findings of this study highlight the platform’s ability to deliver highly accurate results while being versatile and straightforward to adopt across various types of life science laboratories.

Platform Overview

Opentrons Flex is a liquid-handling robot developed for high throughput and complex workflows. The Flex robot is the base of a modular system that utilizes on-deck modules, a labware gripper, pipettes, and labware that are designed to be easily swapped out by the user.

Flex has a touchscreen for working at the lab bench, or it can be controlled with the Opentrons App utilizing open-source APIs from across the laboratory.

Key Features of the Opentrons Flex

• Gripper to Extend Walkaway Time: The Flex Gripper shifts plates and tip racks across the deck and on or off modules. This maximizes throughput and extends walkaway time.
• Accurate Pipettes with Wide Volume Range: Reliable liquid transfers from 1 to 1000 µL using accurate, interchangeable 1, 8, and 96-channel pipettes with extensive volume ranges and automated positional calibration.
• Touchscreen for Easy Protocol Setup: The touchscreen offers select and run practices right from the lab bench and guides the user through deck setup and automated calibration.
• Modules to Fit Your Workflow: Opentrons' modules are designed so that the user can easily integrate them with Opentrons’ robots and software. Choose from the on-deck Thermocycler, Heater-Shaker, Temperature Module and Magnetic Block.

Many choices in Flex workstations incorporate the Flex robot with labware, specific application hardware, and customized practices development:

• Opentrons Flex NGS Workstation automates to the required scale, NGS library prep, increasing efficiency, reducing errors, and saving hands-on time. It automates all pre-sequencing workflows, including tagmentation and fragmentation-based chemistry. 
• Opentrons Flex Protein Purification Workstation automates small-scale protein purification and proteomics sample prep for up to 96 samples. This workstation can be adapted to many magnetic bead-based reagents.
• Opentrons Flex Nucleic Acid Extraction Workstation automates DNA/RNA isolation and purification. This workstation is equipped with the Flex Magnetic Block for separating magnetic beads and the Opentrons Heater-Shaker for sample dissolution and resuspension of magnetic beads.
• Opentrons Flex PCR Workstation fully automates the PCR setup and thermocycling workflow for up to 96 samples. Aliquot chilled reagents and samples into a 96-well PCR plate; the Flex Gripper loads the plate into the on-deck thermocycler on the Flex deck, allowing the PCR program of choice to be run.
• Opentrons Flex Aliquoting Workstation automates the aliquoting of samples or reagents from tubes into 96-well plates. The workstation automates an extremely repetitive and time-consuming task for many laboratories.

Flex workstations have customizable hardware modules and pipette selections to meet the needs of varying workflows (see example deck layouts in Figure 2).

Application Data

Testing was completed using biological samples and popular reagent kits to establish Flex’s capabilities. The testing supported Flex’s potential to provide consistent and precise results for a large variety of applications.

Nucleic Acid Extraction

Nucleic acid extraction can be effectively automated using the Flex. The recommended deck layout includes reservoirs, tip racks, and deep well plates necessary for the high-volume binding and wash steps (Figure 2a).

This combination utilizes the Opentrons Flex Magnetic Block, Opentrons Heater-Shaker Module, and Opentrons Temperature Module for bead pelleting, resuspension, and cooling of sensitive reagents or samples.

The effectiveness of a 48-sample format extraction practice is illustrated in Figure 3. DNA extracted from HeLa cells using the Opentrons Flex exhibits high integrity and purity, making it suitable for downstream applications and analysis, as shown in Figure 3.

Figure 2. Example deck layouts and pipette configurations for three popular applications, (a) nucleic acid extraction,(b) NGS library prep, and (c) small-scale protein purification. Image Credit: Opentrons

Figure 3. Automated nucleic acid extraction from HeLa cells on the Opentrons Flex results in extracted DNA with high average DNA Integrity Number (DIN) and 260/280 absorbance ratio, ready for downstream applications. Image Credit: Opentrons

NGS Library Prep

The Flex efficiently automates the NGS library prep. The workflow combines the on-deck Opentrons Thermocycler Module, Opentrons Flex Magnetic Block, Opentrons Heater-Shaker Module and Opentrons Temperature Module (Figure 2b).

High-temperature enzymatic incubations and indexing can be made on the thermocycler providing stable storage of the sample plate for additional clean-up steps. Utilizing the gripper increases walkaway time, optimizing these complex workflows.

The preparation of NGS libraries with enzymatic fragmentation of genomic E. coli DNA on the Opentrons Flex yielded highly uniform results, as evidenced by the consistent fragment distribution observed in the Tapestation analysis (Figure 4).

The sequenced libraries provided accuracy and highly mappable reads following sequencing on an Illumina^® MiSeq^®.

Protein Purification

Small-scale protein purification utilizing magnetic beads can be easily automated on the Opentrons Flex. The workflow combines the Opentrons Flex Magnetic Block, Opentrons Heater-Shaker Module, and Opentrons Temperature Module for pelleting of protein magnetic beads, resuspension, and cooling of sensitive reagents or samples (Figure 2c).

As demonstrated in Figure 5, automated immunoprecipitation using Protein G beads reproducibly captures the target protein, recombinant GAPDH, with consistent CV across samples.

Figure 4. Expected size distribution, high uniformity, and low coefficient of variation (CV) of NGS libraries constructed from genomic E. coli DNA on the Opentrons Flex. Image Credit: Opentrons

Figure 5. High efficiency and consistent coefficient of variation (CV) across samples for isolation of recombinant GAPDH on the Opentrons Flex. Image Credit: Opentrons

Conclusion

By leveraging the Opentrons Flex for automation, highly accurate and consistent results can be achieved across key life science workflows, including nucleic acid extraction, NGS library preparation, and small-scale protein purification.

The Flex robot can be easily customized with the pipettes, hardware, and labware that laboratory scientists need for diverse applications.

About Opentrons

Today, biologists spend too much time pipetting by hand. We think biologists should have robots to do pipetting for them. People doing science should be free of tedious benchwork and repetitive stress injuries. They should be able to spend their time designing experiments and analyzing data. That's why we started Opentrons.

We make robots for biologists. Our mission is to provide the scientific community with a common platform to easily share protocols and reproduce each other's results. Our robots automate experiments that would otherwise be done by hand, allowing our community to spend more time pursuing answers to some of the 21st century’s most important questions.

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