In an effort to make environmental monitoring more efficient and affordable, the U.S. Environmental Protection Agency (EPA) launched a federal challenge in 2019 to evaluate low-cost, high-throughput RNA sequencing technologies. The goal was to support a new initiative in ecological high-throughput transcriptomics, a field that uses gene expression data to understand how organisms respond to environmental stressors.

Researchers from multiple teams around the world responded to the challenge, each submitting a solution that used RNA samples from four different aquatic species. These methods were evaluated based on how accurately and consistently they captured gene activity, how much of the transcriptome they covered, how affordable they were per sample, and how many samples could be processed at once.

The top-ranking method, submitted by a team using the TempO-Seq platform, focused on sequencing only selected sentinel genes rather than the full transcriptome. This targeted approach represented just 5–11% of the full gene set but still produced results closely aligned with full RNA sequencing data, often within a tenfold range. That’s a significant finding for regulatory toxicology and environmental science, as it shows targeted RNA sequencing can be a practical and cost-effective alternative for large-scale ecological studies.

A team led by researchers at the EPA Great Lakes Toxicology and Ecology Division concluded that multiple RNA sequencing technologies are viable for use in ecological transcriptomics, each offering unique strengths depending on the goals of the study. The key takeaway is that transparency in how data are collected and reported will be critical to encouraging broader adoption of these methods in environmental decision-making.