Automating Oligo Plating: A Representative System for Quantification, Normalization & QC

Oligonucleotide synthesis and plating workflows demand both flexibility and precision. In many synthetic biology and reagent production labs, scientists need to normalize sample concentrations, perform QC, and plate oligos at scale, often with limited staff and high variability in sample inputs.

At HighRes, we work with labs like these to design modular automation systems that not only execute complex protocols but also adapt to evolving throughput and traceability requirements. This write-up explores a representative system architecture for an oligo plating workflow, designed to support quantification, normalization, and QC processes across 10+ plates per day.

Figure 1. Automated oligo plating system featuring the Prime Liquid Handler.

Workflow Goals: Efficient, Traceable Oligo Handling

Figure 2. CellarioScheduler Protocol for Automated Oligo Plating

This representative system was designed to meet common needs across oligo manufacturing and synthetic biology workflows, including:

• Quantification of master oligos using plate reader data
• Normalization of individual wells based on file-driven dilution logic
• Quality Control (QC) to confirm concentration accuracy
• Automated plating of normalized oligos for storage or downstream applications

The operational goal was to process ~10 deep-well plates per day with minimal operator touchpoints, enforcing QC steps and optimizing consumable usage.

System Architecture: Modular, Expandable, and Prime-Based

The system is anchored by the Prime Liquid Handler and integrates a range of devices to enable fully automated oligo plating and QC.

Figure 3. Automated Oligo Plating System Design

Key Components:

• HighRes’ Prime Liquid Handler includes storage and integrated robotic arm to allow for a compact yet scalable layout that supports simultaneous runs and on-deck buffering of consumables and samples.
  • High-speed pipetting (iZ8 head) with CSV-driven transfer logic
  • 96-Channel Pipetting Head for high-throughput plate processing
  • PSP & Autofill Reservoirs, external tip waste, and waste bins
• Tecan Infinite M200 Nano for absorbance-based quantification
• Agilent PlateLoc for plate sealing
• Scinomix Sciprint for plate barcoding and reading
• Expansion-ready modules such as Azenta XPeel, Unchained Labs Lunatic, and MicroSpin for future scaling

Workflow Considerations: Custom Logic and Tip Reuse

This system example highlights two technical considerations we often address in oligo workflows:

• CSV-Driven Transfers: The normalization protocol prompts users to upload a CSV file at run start, which dynamically controls the iZ8 pipette transfers. This enables accurate, sample-specific dilution based on real-time data or upstream calculations.
• Controlled Tip Reuse: To reduce plastic waste without compromising integrity, the method was configured to use each tip twice, once for diluent, once for oligo transfer. Tip usage tracking is built into the execution logic.

Combined, these features support both sustainability and accuracy, which is critical for labs balancing cost, scale, and compliance.

Smart Scheduling with CellarioScheduler: Optimizing Throughput with Parallel Execution

One of the most powerful enablers of this workflow’s throughput is CellarioScheduler, HighRes’ built-in scheduling engine that automates multistep workflows across devices in parallel.

For this oligo plating example, CellarioScheduler visualizes runs using a Gantt chart, where each device’s timeline is dynamically updated to reflect resource usage across 10 simultaneous plates.

Figure 4. CellarioScheduler Protocol Simulation

Benefits of Intelligent Scheduling:

• Parallelization: Devices like the iZ8, reader, and sealer operate concurrently across plates, maximizing system utilization.
• Bottleneck Avoidance: Scheduler proactively staggers plate handoffs to avoid idle time or traffic jams in shared modules.
• Scalability: As demand increases, the system can scale up to more plates/day with little to no change in user burden.
• Visibility: The Gantt view provides real-time insight into system flow, helping operators anticipate completion times and intervene when needed.

By leveraging CellarioScheduler’s capabilities, this system supports consistent daily runs while making the most of limited lab space and resources.

Software Integration: Ready for CellarioOS Orchestration

The system is designed to be compatible with CellarioOS, enabling full orchestration of multistep workflows, integration with LIMS, and traceability across quantification and QC events. In this representative build:

• Data from the plate reader informs transfer volumes
• Sample lineage is maintained across normalization and QC
• Future scripting or protocol logic can be handled externally or within CellarioOS

Whether the workflow is manually initiated or fully scheduled, the software architecture enables labs to grow without introducing unnecessary complexity.

Summary: What This Example Shows

This representative system illustrates how HighRes approaches oligo plating workflows with flexibility, performance, and future scalability in mind. Every detail, from how CSV files drive sample-specific normalization to how plate hotels enable uninterrupted throughput, is rooted in deep experience across the life sciences.

We don’t just automate. We co-design workflows that improve lab productivity, reduce risk, and scale with your science.

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