10x Genomics has begun shipping its latest Flex assay for its Chromium instrument platform, responding to the needs of the single-cell sequencing market for easy to use, higher-throughput and scalable solutions. For example, the burgeoning field of cell atlases, or maps of an organism’s cells, requiring larger data sets and thus the faster generation of single-cell data at a lower cost. Larger data sets also enable training of AI models for data analysis.

The next-generation Flex assay can also grow the market for single-cell sequencing in general by providing greater accessibility to all labs with its more affordable, easy to use and flexible format. For example, the number of samples that can be run at one time accommodates a lab’s changing needs. Also, the assay can be used with a variety of  fresh, frozen and PFA-fix tissues, as well as with FFPE samples. It can also measure protein coding and generation expression using fixed and batch workflows.

Founded in 2012 and considered a pioneer in single-cell transcriptomics, 10x Genomics completed its IPO in 2019 and last year generated revenues of $610 million. The company provides both single-cell platform analysis and high-resolution spatial gene expression platforms.

IBO interviewed Michael Schnall-Levin, Ph.D., Chief Technology Officer, Founding Scientist of 10x Genomics, about the next-generation Flex assay.

IBO: What are some examples of the improved ease of use of the new assay?

Dr. Schnall-Levin: The ability to multiplex in a plate-based format offers more streamlined sample handling, amenable to automation. The new Flex enables convenient batching with the ability to pool anywhere from two to 384 samples without waste.

IBO: Can you give an example of the type of translational research expected to benefit immediately from this solution?

Dr. Schnall-Levin: The type of translational research expected to benefit immediately from Flex v2 is large-scale clinical trial monitoring and biomarker discovery in oncology and immunology. The core value of Flex v2 lies in its scalability and flexibility, which are essential to meet the diverse needs of different translational research labs.

IBO: Around what percentage of current 10x assay users do you think are looking for this kind of scale to meet their research needs?

Dr. Schnall-Levin: We are seeing strong interest across the board. Many existing customers have already proven the value of single-cell data in smaller experiments, and now they want to extend these insights across hundreds of samples or larger cohorts. So while not everyone needs that scale today, it is becoming an increasingly common goal.

IBO: What was the biggest challenge in adapting the Flex assay to a 96 well-plate format?

Dr. Schnall-Levin: The most challenging aspect was making this assay truly scalable without adding complexity. Moving to a plate-based format introduced new challenges around multiplexing at much higher sample numbers. We focused on engineering a diverse barcode set that supports reliable multiplexing of 384 samples, simplifying hands-on steps to minimize technical variability and maintaining the same high-quality data that customers expect from 10x.