MERCURIUS™

DRUG-seq 

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 are 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 protocol

Improved protocol, leading to 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

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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.

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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.
100%
Unbiased whole transcriptome screening

No need for prior target selection.

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Pre-amplification free protocol

No pre-amplification needed, leading to higher mapping and gene detection rates.

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One-day lab workflow
Convenient and quick protocol, from samples to sequencing-ready libraries in one day.
Money
Ultra scalable and ultra low-cost 

The more samples processed simultaneously, the lower the cost per sample.

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

A transformative tool for next-gen drug discovery

A scalable and cost-effective transcriptomic profiling solution that accelerates target identification and validation, hit identification, hit-to-lead, and lead optimization.
By providing deep gene expression insights across thousands of compounds, MERCURIUS™ DRUG-seq reveals mechanisms of action, detects on/off-target effects, and uncovers toxicity markers, empowering faster, data-driven decisions throughout the drug development pipeline.
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Decoding drug responses

MERCURIUS™ DRUG-seq empowers scalable transcriptome profiling by enabling precise gene detection, characterization of drug-response signatures, identification of synergistic/antagonistic drug effects, detailed pathway-level insights and much more.
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Gene detection overview

Gene detection overview of a case study on 22'000 samples and 51 compounds in four doses, on 6 cell lines, sequenced at 1M reads per sample. 

Enables accurate clustering and co-clustering analysis based on unbiased gene expression measurement

Analysis of top DE genes
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Detect potential synergistic/antagonistic effects of drug combinations

Enables detailed pathway analysis of biological processes

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More applications

  • Mechanism

    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!
     
  • resistance

    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. 
     
  • Toxicity@300x-50

    Toxicology and safety assessment

     

    MERCURIUS™ DRUG-seq is a powerful tool for transcriptome-wide toxicology studies, enabling high-throughput phenotypic screening, cell response screening, and compound activity profiling.
     
    The technology captures comprehensive gene expression changes across thousands of conditions to help identify early toxicity signals, stress responses, and off-target effects. Whether used alone or in combination with CRISPR screens, MERCURIUS™ DRUG-seq provides the resolution and scalability needed to assess compound safety at every stage of drug discovery and to accelerate the development of safer, more effective therapeutics.
  • AI@300x-50-3

    AI-driven drug discovery

     

    Artificial intelligence algorithms require vast quantities of robust, in-depth training data for pattern recognition and predictive modeling before researchers can extract meaningful insights with confidence. The unparalleled scalability and cost-effectiveness of MERCURIUS™ DRUG-seq now enables researchers to generate high-throughput transcriptome-wide data for thousands of samples or conditions. These data help to train advanced machine learning models and deep learning algorithms, streamlining screening pipelines and enabling smarter, faster compound discovery.

    This integration facilitates scalable phenotypic screening and compound similarity mapping, accelerating mechanism of action identification, target deconvolution, and gene network analysis. Leveraging AI-powered pattern recognition and predictive modeling, researchers can extract meaningful gene signatures and uncover novel biomarkers with greater confidence.

     

Diverse readout options

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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.
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Targeted mRNA sequencing

Focuses on sequencing specific genes rather than the whole transcriptome.
 
Increases sensitivity and depth for studying low-abundance transcripts.
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Full-length mRNA sequencing

Capture complete transcript information by sequencing the entire length of mRNA molecules, from 5′ to 3′.

This protocol enables comprehensive analysis of transcript isoforms, alternative splicing events, and gene expression levels. 
 

Available as kits and services

 

Kits for library prep

All our kits contain all the oligos and enzymes needed to go from 2D cell cultures / 3D organoids and spheroids to sequencing-ready libraries.

 

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
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MERCURIUS™

Total DRUG-seq (Early-Access)

  • Full-length total RNA sequencing
  • 96 and 384 samples multiplexing format
  • Directly from cell/organoid lysates without prior RNA isolation
  • 20'000 + genes detected at 10M reads/sample
  • Full-length RNA transcript coverage: for regulatory RNAs, non-coding RNAs, and early-stage transcripts.
FIND OUT MORE

MERCURIUS™

Full-Length

DRUG-seq kit (Early-Access)

  • Full-length mRNA sequencing
  • 96 samples multiplexing format
  • Directly from cell/organoid lysates without prior RNA isolation
  • 22'000 genes detected at 12M reads/sample
  • Full-length mRNA transcript coverage: from differential gene expression to splicing variants and isoform detection
Find out more
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Flexible Services

From library prep only or end-to-end service, including cell culture and treatment, Cell Painting, NGS and downstream analysis.

 

What do our customers say

 

 

 

" 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