DRUG-seq technology

Unbiased whole transcriptome screening

MERCURIUS™ DRUG-seq is a powerful solution for compound screening and drug discovery, enabling ultra-high-content, unbiased, and high-throughput profiling with extraction-free transcriptomics. The method leverages rigorously optimized sample barcodes and unique molecular identifiers (UMIs) to label the 3' poly(A) tails of mRNA molecules during the first-strand cDNA synthesis. This efficient tagging approach ensures precise sample identification, robust transcript quantification, and seamless scalability for large screening campaigns.

Extraction-free

Skip tedious RNA extraction steps and go straight to library prep.

Cell lysis buffers are highly optimized for 2D cell cultures and organoid models to generate library preps efficiently without prior RNA isolation.

Massive sample multiplexing

Up-to 384 samples processed in one single tube!

Our highly optimized sets of barcoded primers uniquely "tag" individual RNA samples during the first step of library preparation so that you can pool and process all samples together in a single tube early in the workflow.

Pre-amplification-free

Improved protocol for higher mapping and gene detection rates

MERCURIUS™ DRUG-seq leverages a high-yield enzyme for reverse transcription. This streamlines the workflow and eliminates potential biases and duplication introduced with pre-amplification and template-switching oligos (TSO) used in the original DRUG-seq protocol while delivering superior performance.

Benefits

Ideal for screening projects: Massively multiplexed workflow with 96 and 384-well plate formats so that you can screen thousands of samples in parallel at scale.

No need for prior RNA extraction: An optimized lysis buffer ensures complete lysis and efficient reverse transcription to avoid time-consuming and expensive RNA extractions.

Unbiased whole transcriptome screening: No need for prior target selection.

Pre-amplification free protocol: No pre-amplification needed, leading to higher mapping and gene detection rates.

One-day lab workflow: Convenient and quick protocol, from samples to sequencing-ready libraries in one day.

Ultra scalable and ultra low-cost: The more samples processed simultaneously, the lower the cost per sample.

Suited to automation: Enables seamless integration into high-throughput workflows, furter reducing hands-on time and increasing scalability, reproducibility and efficiency.

MERCURIUS™ DRUG-seq accelerates the journey from target discovery to validation due to its scalability, sensitivity, and depth.

It allows you to select targets with desirable transcriptomic signatures and confirm that modulating a specific target leads to the expected changes in gene expression.

MERCURIUS™ DRUG-seq provides cost-effective deep transcriptomic insights that help identify the most promising compounds in screening pipelines with greater confidence.

Hit-to-lead optimization is streamlined by rapid and scalable assessment of gene expression changes across thousands of compounds or conditions simultaneously.

MERCURIUS™ DRUG-seq's ability to detect novel transcripts and mechanisms of action enhances the understanding of drug interactions at a molecular level. This makes it an invaluable tool for optimizing leads and advancing the development of effective and safe therapeutics.

MERCURIUS™ DRUG-seq rapidly allows researchers to detect on- and off-target effects, uncover toxicity markers, and track transcriptional changes across thousands of compounds or conditions. This knowledge speeds up the drug development process, enhances decision-making, and increases the likelihood of therapeutic success in drug development.

More applications

Mechanism of disease and biomarker discovery

MERCURIUS™ DRUG-seq streamlines ultra-high-content and high-throughput transcriptomic profiling, enabling the rapid and cost-effective identification of disease pathways and key regulatory genes, which can be later used as diagnostic or prognostic biomarkers.

Discover biomarkers faster and with greater confidence to transform data into actionable insights!
Drug resistance

MERCURIUS™ DRUG-seq can also be used to identify drug resistance mechanisms at the transcriptomic level.

This enables researchers to pinpoint molecular adaptations, predict responses, and develop more effective therapeutic strategies.

Diverse readout options

3' mRNA sequencing

Focused on sequencing only the 3′ end of mRNA molecules.

Provides a cost-effective and scalable way to measure gene expression levels across thousands of samples.

Targeted mRNA sequencing

Focuses on sequencing specific genes rather than the whole transcriptome.

Increases sensitivity and depth for studying low-abundance transcripts.

MERCURIUS™

DRUG-seq kit

3' mRNA sequencing
Early multiplexing of up to 384 samples
Directly from cell lysates without prior RNA isolation
12'000 genes detected at 1M reads/sample
Ideal for comprehensive genome-wide gene expression profiling

Find out more Download brochure

A Transformative Tool for Drug Discovery

Gene detection overview

Gene detection overview of a case study on 12'000 samples and almost 4'000 compound combinations, sequenced at 1M reads per sample.

Analysis of top DE genes reveals signature of drug response in combinatorial treatment context

MERCURIUS™ DRUG-seq can detect potential synergistic /antagonistic effects of drug combinations

MERCURIUS™ DRUG-seq enables detailed pathway analysis of biological processes.

" We would be glad to work together again"

The DRUG-seq platform enabled us to systematically profile compound-induced transcriptional responses at scale, generating a rich dataset that helped prioritize testable hypotheses. The team at Alithea provided outstanding technical guidance throughout, including support in developing a customized analysis pipeline tailored to our needs. The turnaround time was fast, the process seamless, and the collaboration highly productive. We would be glad to work together again.

Mikołaj Słabicki, Ph.D. Principal Investigator at the MGH Krantz Family Center for Cancer Research. Assistant Professor of Medicine at Harvard Medical School. Affiliate Faculty Member at the Broad Institute of MIT and Harvard

"It's fast, scalable, and incredibly cost-effective"

DRUG-seq has completely transformed how I approach and think about transcriptomic screening. It's fast, scalable, and incredibly cost-effective—perfect for profiling hundreds of compounds in parallel. In my experience, it’s one of the most powerful tools for uncovering mechanisms of action and capturing transcriptional signatures at scale. I've used DRUG-seq to profile different cells treated under time points, dose responses, combination treatments, and a variety of complex cellular models, from cardiomyocytes to organoids—and it consistently delivers high-quality, actionable data. The ability to pool samples early without compromising data quality truly makes it a game-changer.

Andrea Hadjikyriacou, Ph.D. Principal Scientist I, Novartis Biomedical Research

FAQ

MERCURIUS™ DRUG-seq is a transformative tool for compound screening and drug discovery, combining unbiased, ultra-high-content, and high-throughput compound screening with massively parallel and extraction-free transcriptomics. This metho d uses highly optimized and rigorously evaluated sample barcodes and unique molecular identifiers to tag the 3’ poly(A) tail of all mRNA molecules in a sample-specific manner during the first-strand synthesis step of cDNA library preparation.

The DRUG-seq protocol is designed to work with frozen cells and bypass RNA extraction. Thanks to the highly optimized lysis buffers for cell lysis of 2D cell cultures and organoid models, it efficiently generates library preps without prior RNA isolation.
Unlike the original DRUG-seq protocol, which relies on the use of template-switching oligos (TSO) and pre-amplification for the second-strand cDNA synthesis, the MERCURIUS™ DRUG-seq streamlines the workflow by performing the reverse transcription with a high-yield enzyme, thus eliminating the potential biases and duplication introduced with pre-amplification.

This optimized workflow not only simplifies the protocol but also delivers superior performance: higher mapping and gene detection rates.
MERCURIUS™ DRUG-seq stands out from traditional RNA-seq methods by offering a high-throughput, cost-efficient, and streamlined workflow specifically designed for large-scale screening applications. One of the key differences lies in its sample multiplexing strategy: DRUG-seq allows multiple RNA samples to be barcoded and pooled at the earliest step of the protocol—right after cell lysis—so that the entire library preparation can proceed in a single tube. This significantly reduces both hands-on time and reagent costs.

In contrast, standard RNA-seq workflows typically require individual RNA extraction and processing for each sample, followed by separate library preparations. This makes them more labor-intensive, costly, and less scalable, especially when working with large numbers of conditions, compounds, or replicates—common in drug discovery pipelines.
MERCURIUS™ DRUG-seq is used for:

Drug discovery: Identifying new drug candidates and understanding how existing drugs work at a molecular level.

Mechanism of action studies: Understanding how drugs affect cellular pathways and gene regulation.

Drug repurposing: Identifying new uses for existing drugs based on gene expression changes.

Personalized medicine: Tailoring treatments based on individual genetic responses to drugs.

DRUG-seq technology

Unbiased whole transcriptome screening

Extraction-free

Massive sample multiplexing

Pre-amplification-free

Benefits

Applications

More applications

Mechanism of disease and biomarker discovery

Drug resistance

Diverse readout options

3' mRNA sequencing

Targeted mRNA sequencing

Available as kits and services

Kits for library prep

DRUG-seq kit

Flexible Services

Package 1

Package 2

Package 3

A Transformative Tool for Drug Discovery

Gene detection overview

Analysis of top DE genes reveals signature of drug response in combinatorial treatment context

MERCURIUS™ DRUG-seq can detect potential synergistic /antagonistic effects of drug combinations

MERCURIUS™ DRUG-seq enables detailed pathway analysis of biological processes.

What do our customers say

" We would be glad to work together again"

"It's fast, scalable, and incredibly cost-effective"

Recent blogs

Overview of Published 3’ mRNA-seq Workflows: From Early Multiplexing and Beyond

Published Bulk 3’ mRNA-seq Technologies: Which is Best for Your Next Screen?

Maximizing Drug Discovery with High-Throughput and High-Content Screening

Recent publications

FAQ