New ultra-high-throughput kit enables discovery teams to generate transcriptome-wide compound-response data directly from 1536-well plates

Alithea Genomics today announced the early access launch of MERCURIUS™ 1536 DRUG-seq, a new ultra-high-throughput transcriptomics kit designed to help drug discovery teams profile compound-induced biological responses at true screening scale.

The launch addresses a growing challenge in pharmaceutical R&D: discovery teams can now screen large compound libraries with increasing speed and automation, but they often rely on narrow assay endpoints that reveal whether a compound has an effect without providing sufficient biological context into why that effect occurs. Transcriptomics can provide that deeper view, but until now it has often been too costly, complex, or low-throughput to deploy across large screening campaigns.

MERCURIUS™ 1536 DRUG-seq is designed to close that gap. By enabling transcriptome-wide gene expression profiling directly from 1536-well plates, the new kit gives researchers a practical way to generate standardized biological response data across compounds, concentrations, time points, and cellular models.

“The bottleneck in drug discovery is no longer only the ability to screen more compounds. It is the ability to understand biological response at the same scale,” said Frederik Decouttere, CEO of Alithea Genomics. “MERCURIUS™ 1536 DRUG-seq was developed to make transcriptomics compatible with the scale of modern screening, giving teams richer evidence earlier in the discovery process, helping to accelerate the therapeutic programs, protecting downstream budgets by avoiding late-stage pivots.”

The new kit extends Alithea’s MERCURIUS™ DRUG-seq platform to 1536-well workflows. Cell lysis and barcoded reverse transcription are performed directly in the 1536-well culture plate, followed by pooling of all 1536 samples into a single tube for downstream library preparation. This miniaturized, pooled workflow is designed to reduce hands-on time, support automation, and limit batch effects while preserving the depth and biological resolution needed for transcriptomic screening.

MERCURIUS™ 1536 DRUG-seq is intended for discovery teams working on large-scale compound profiling, mechanism of action discovery, toxicity assessment, benchmark dosing, compound prioritization, and the generation of structured perturbation datasets for AI-driven drug discovery. It also provides a complementary molecular readout for high-content imaging workflows, including Cell Painting.

Early performance data demonstrate high demultiplexing efficiency, consistent gene detection across 1536-well plates, and robust capture of compound-induced transcriptional responses. In internal validation studies, MERCURIUS™ 1536 DRUG-seq assigned more than 96% of reads to individual samples and detected more than 12,000 genes at only 0.7 million reads per sample. The technology also showed reproducible differential expression signatures across independently processed plates and resolved mechanism-specific toxicity responses across compounds.

MERCURIUS™ 1536 DRUG-seq is designed for cell lines and primary cells in 1536-well assay plates, with input requirements of 400 to 1,000 mammalian cells per well. The workflow supports approximately 2.5 hours of hands-on library preparation time and does not require a 1536-well thermocycler, helping remove a practical bottleneck for laboratories working in highly miniaturized screening formats.

“AI-driven discovery depends on the quality, scale, and structure of the biological data used to train and interpret models,” said Frederik Decouttere, CEO at Alithea Genomics. “With MERCURIUS™ 1536 DRUG-seq, researchers can generate large transcriptomic datasets that connect chemical perturbation to biological response across screening-scale experiments.”

MERCURIUS™ 1536 DRUG-seq is compatible with Illumina®, Ultima Genomics, and AVITI™ sequencing instruments. The kit is available in a 1536-prep format through Alithea Genomics’ early access program.

Alithea Genomics is now inviting interested early access users to join the launch webinar on June 24^th and learn more about the product.

For more information, visit the MERCURIUS™ 1536 DRUG-seq product page.

About MERCURIUS™ 1536 DRUG-seq

MERCURIUS™ 1536 DRUG-seq is an ultra-high-throughput 3′ mRNA-seq technology designed for transcriptomic profiling directly from 1536-well assay plates. The workflow performs cell lysis and barcoded reverse transcription directly in the culture plate, followed by pooling of 1536 samples into a single tube for downstream library preparation.

MERCURIUS™ 1536 DRUG-seq enables screening teams to generate large, standardized compound-response datasets for primary screening, mechanism of action discovery, toxicity profiling, benchmark dosing, compound prioritization, Cell Painting complementarity, and AI-driven drug discovery.

About Alithea Genomics

Alithea Genomics develops scalable RNA-seq technologies that simplify the generation of large, high-quality transcriptomic datasets. The company’s MERCURIUS™ platform family includes DRUG-seq, BRB-seq, and FLASH-seq technologies, enabling high-throughput RNA profiling for drug discovery, biomarker research, toxicology, and large-scale biological discovery.

Founded at EPFL in Lausanne, Switzerland, Alithea Genomics serves pharmaceutical, biotechnology, CRO, agritech, cosmetics, core facility, and academic research teams worldwide, helping them generate thousands to millions of gene expression profiles at the scale their biological questions demand.