Generating the largest scRNA-seq datasets in the world with automated pipetting
Single-cell RNA sequencing for drug discovery
Tahoe Therapeutics (formerly Vevo Therapeutics) was founded in 2022 with the aim of using scRNA-seq to create the world’s largest atlas describing how drugs interact with patient cells. The company already has several programs running in parallel across multiple cancer types and is now expanding into other therapeutic areas including cardiovascular, metabolic and neurodegenerative diseases.
Tahoe Therapeutics chose this approach because scRNA-seq results in greater amounts of data than conventional sequencing workflows, as Johnny Yu, Cofounder and Chief Scientific Officer, explained: “scRNA-seq offers an enhanced understanding of the diverse drug responses of different cell types, which cannot be easily elucidated using conventional bulk sequencing. We use a high throughput method to generate a lot of data at the single-cell level, and our first dataset – Tahoe 100 million – was the largest in the field ever. It effectively doubled the size of all the publicly available data generated over the last decade.”
Automation to improve workflows
Tahoe Therapeutics has developed its own biological assays using complex biological model systems. The company uses Evercode kits from Parse Biosciences to perform scRNA-seq, ensuring scalable data generation to inform its drug discovery models. Its stated aim of creating the largest scRNA-seq datasets in the world makes lab automation essential for the team. “We quickly realized that, as we were generating more and more data and pushing the limits of the field, we were missing robotic and high throughput solutions,” said Johnny.
INTEGRA’s partnership with Parse Biosciences made its solutions the clear first choice for the automation needs of Tahoe Therapeutics, providing validated, turnkey solutions covering every stage of scRNA-seq sample preparation. Johnny and the team use the ASSIST PLUS pipetting robot with the 8 channel VIAFLO handheld electronic pipette to automate the Evercode sc-RNA-seq workflow. “One of the main benefits of the ASSIST PLUS pipetting robot is its flexibility. The system is supplied with a built-in protocol for the Parse Evercode single cell workflow, and we were quickly able to program it for several different things beyond scRNA-seq sample preparation,” explained Johnny. “This is important as in our small lab, as we’re running a lot of different protocols.” For a small team with diverse skillsets, intuitive programming for multiple tasks is crucial. “One thing that sets the ASSIST PLUS apart from other, more expensive, automated solutions is that you don’t have to be an automation engineer with years of experience with the system,” said Johnny. “We have two methods developers working on the system with no prior automation background, and they are able to quickly roll out new methods to the rest of our team.”
The team’s workflows are tightly coordinated to exact timepoints, and live cells must be rapidly yet gently manipulated. The speed of INTEGRA’s automated solutions, combined with Parse Biosciences’ products, means that a large number of biological samples can be processed in parallel. The speed, accuracy and reproducibility of this set-up will be crucial as Tahoe Therapeutics scales up its research to generate a dataset 50 times larger than the record-breaking Tahoe 100 million. “Automation has increased our throughput for data generation more than 5-fold for the single-cell preparation part of our workflow,” explained Johnny. “The most important thing is that it’s highly accurate: you’re not relying on the inherent variability of manual processing.”
Exceptional customer service and support
INTEGRA’s automated lab solutions have become essential for the company’s work, so a high level of customer service and support is vital. The Tahoe Therapeutics team benefits from rapid responses to technical queries at all times of the day, as well as tailored procurement advice to help streamline their workflows. “Service and sales are tightly integrated at INTEGRA, which I find very beneficial,” explained Johnny. “I know our sales rep by name – I even once contacted her while she was on a flight – and I trust her to be on our team’s side to find the correct solution to the problems at hand. I think that relationship is one of the things that sets INTEGRA apart.”
A unified platform for liquid handling and next generation sequencing
INTEGRA’s automated pipetting robots, combined with Parse Biosciences’ single cell protocols, have provided a unified approach for Tahoe Therapeutics. The powerful yet intuitive nature of programming the ASSIST PLUS, combined with the excellent support from INTEGRA, has allowed the company to push the boundaries of the field and stay ahead of competitors using older technologies. “A lot of the latest biopharmaceutical work is still based on bulk RNA sequencing – a method from a decade ago,” said Johnny. “The technology we use allows us to leapfrog many biopharmaceutical companies and generate larger datasets using less instrumentation, reagents and capital.”