How An Automated On-Deck Thermocycler Saves Your Lab Time, Part 3: NGS Library Prep Case Study

This post is an excerpt from our 10-page "How To Save Time In The Lab With An Automated On-Deck Thermocycler" e-book. Click here to download the e-book.

If your lab is already automating workflows ranging from genotyping and sequencing to cloning and gene-editing, adding an on-deck thermocycler to your liquid handling robot can increase your free time by a factor of 3x.

The protocols that get the most out of integrating a thermocycler are complex, involving multiple sub-protocols before and after an incubation or PCR step. Let’s look at a next-generation sequencing (NGS) library preparation protocol as an example.
Figure-3
By automating only the pipetting and magnetic bead handling steps in the workflow, you take approximately ⅔ of the work off your hands. That's the enzymatic prep (fragmentation + a-tailing, etc.), cleanups, indexing, and pooling steps, which can be done by the OT-2 liquid handling robot with the Opentrons Magnetic Module.

Without a thermocycler on the deck of your robot, a person (or another, more expensive robot) has to physically move the prepared reactions into the thermocycler. After the amplification is complete, they also need to physically retrieve the samples—taking them off of the thermocycler and putting them back on the robot for the final magnetic and pipetting steps.

While each of the three blocks of two-hour processes is automated, there is required human intervention between the automated steps, preventing you from benefiting from all your saved time at once.

Adding an on-deck thermocycler for the amplification step in the middle of NGS library prep process removes the need for human intervention between steps creating an end-to-end automated workflow. Fragmentation, A-tailing, ligation, amplification, and clean-up + pooling are all automated in one run, giving you a single six-hour block of uninterrupted free time.
Figure-2-1-1
Figure-2-2-1
This post is an excerpt from our 10-page "How To Save Time In The Lab With An Automated On-Deck Thermocycler" e-book. Click here to download the e-book.