A Revolution in Evolution: Years of Work Distilled to One Onyx Experiment

Let’s say you have used the Onyx Digital Genome Engineering platform to generate a library of hundreds, if not thousands, of edits that results in a wellspring of biochemical information.

Now what?

In a recent webinar, Inscripta senior scientist Tyson Shepherd walked the audience through not only the Onyx technology and workflow, but also how the resulting data could be analyzed to either confirm existing knowledge or generate new discoveries.

He shared an example of the data collected from a library of 992 engineered and trackable E. coli strain variants used to test for small molecule tolerance and sensitivity. In this work, Inscripta scientists recapitulated an E. coli library of 372 previously described mutations from an Adaptive Laboratory Evolution (ALE) experiment done by Markus Herrgard’s lab at DTU Biosustain. Moreover, they generated an additional 620 deletions, frameshifts, and mobile element insertions as functional knockouts.

“In about a week’s time, you can go from engineered cells to data,” Shepherd said. “The true excitement comes once you receive the sequencing results and you get to dive into all of this great data. There’s about a thesis’s worth of data for every run of the Inscripta Onyx.”

The first thing to do with the data — assisted by the InscriptaRevolver software — is to assess its quality and reproducibility across triplicates, and across the different conditions. Then, look for key differences between those conditions, specifically for trends in enrichments and depletion.

Thanks to the trackable barcodes in the pooled libraries, it is easy to see the responses for every single edit and do functional assessments, Shepherd said. The platform’s built-in bioinformatics tools provide several ways to visualize the data, such as using barcode abundance to measure tolerance, or examining profile clusters of replicates and conditions to highlight distinct biological responses.

“There’s so much distinct biology that’s ripe for digging into,” Shepherd said.

“The Onyx platform provides a way to go way beyond what an ALE experiment could typically do,” he added. “In just a few weeks of bench time, you can recapitulate months, or even years of work. That’s going to enhance your overall data collection, and also enhance new biochemical discoveries that you can take forward and make meaningful impacts with.”