DRUG-seq technology

MERCURIUS™ FLASH-seq provides full-length mRNA transcript coverage even for low-abundance genes, empowering researchers to explore differential gene expression, detect alternative splicing, and analyze isoform diversity—all critical for understanding complex biology, especially in rare cell populations.

The technology is based on the method first published in Nature Biotechnology, which offers unmatched sensitivity and reduces hands-on time compared to Smart-seq2 and Smart-seq3.

The MERCURIUS™ FLASH-seq protocol achieves these improvements in speed and sensitivity by combining the reverse transcription (RT) and cDNA preamplification stages, harnessing a more processive reverse transcriptase with a shortened RT reaction time, and enhancing the template-switching reaction crucial for full-length cDNA synthesis.

Benefits

Ultra-sensitive: Up to 2x more genes detected than other commercially available solutions. Ideal for rare cell capture.

For low-input RNA: From as low as one cell or 1-100 pg input.

Full-length transcript coverage

From differential gene expression to splicing variants and isoform detection.

No need for prior RNA extraction: Simply FACS-sort the cells in the wells containing the buffer for complete lysis and efficient reverse transcription.

One-day lab workflow: Convenient and short protocol from samples to sequencing-ready libraries in only 7H30.

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

Applications

Cancer Research

Dissect tumor heterogeneity by sequencing rare cancer stem cells or circulating tumor cells. FLASH-seq offers the resolution and sensitivity to enable detection of expressed mutations, splicing isoforms, and gene fusions, providing deep insights into clonal evolution and therapeutic resistance in individual cancer cells.
Developmental Biology

By mapping gene expression trajectories across individual cells during early development, FLASH-seq allows researchers to study how cells differentiate and form tissues, helping to unravel the complex processes that drive organismal development.
Neuroscience

The brain consists of a vast array of cell types, each with distinct roles. FLASH-seq can map the transcriptomic landscape of these cells, contributing to a deeper understanding of neuronal functions and the molecular mechanisms underlying neurological disorders.

The protocol has been successfully used to sequence rare, sorted cell types in the retina or brain, as well as sub-cellular content.
Immunology

The immune system’s complexity lies in the diverse cell types it comprises. FLASH-seq can track gene expression in immune cells, offering insights into how the immune system responds to infections, autoimmune disorders, and other diseases. Moreover, TCR chains and CDR3 variable regions can be inferred at the single-cell level from FLASH-seq data without any additional processing.

Importantly, FLASH-seq also enables the detection of transcriptomes from intracellular viruses such as retroviruses or adeno-associated viruses (AAVs), providing a powerful approach to study host–virus interactions directly at the single-cell level.
Sub-cellular content

The sensitivity of FLASH-seq makes it efficient even with sub-cellular amounts of RNA (<1 pg) such as exosomes preparations or biopsies of individual cells.
Genetic Therapies & ASOs

Researchers can use FLASH-seq to evaluate the effect of antisense oligonucleotides (ASOs) on target splicing at single-cell resolution. This enables precise tracking of treatment efficacy across rare or responsive cell subsets within a population.

Performance

FLASH_seq-highest sensitivity in gene detection

MERCURIUS™ FLASH-seq shows the highest sensitivity in gene detection

The number of detected genes in HEK 293T cells processed with different protocols. Reads were downsampled to 500,000 raw reads.

The MERCURIUSTM FLASH-seq sensitivity is retained even in highly heterogeneous populations

The sensitivity of MERCURIUS™ FLASH-seq is retained even in highly heterogeneous populations

Number of genes detected in human PBMCs, processed with different protocols, and the number of reads downsampled to 125,000 raw reads.

MERCURIUS™ FLASH-seq is a full-length scRNA-seq protocol

Gene body coverage shows a uniform read distribution across the entire gene body for the FLASH-seq protocol.

MERCURIUS™ FLASH-seq shows high sensitivity for low sample inputs

The number of genes detected in HEK 293T cells using different RNA inputs (from 2.5 pg to 250 pg) at different sequencing depths.

FLASH-seq discriminates between rare cell populations

MERCURIUS™ FLASH-seq can discriminate rare cell populations in heterogeneous samples

UMAP of hPBMC, automatically annotated using Azimuth (Hao et al, 2021).

MERCURIUS™

Single-cell

FLASH-seq kit

Single-cell full-length mRNA sequencing
Ultra-sensitive and rapid
Plate-based
Ideal for rare cell capture and isoform detection

Find out more

MERCURIUS™

Low-input

FLASH-seq kit

From 1 pg RNA input
Ultra-sensitive and rapid
Plate-based
Ideal for rare cell capture and isoform detection

FIND OUT MORE

MERCURIUS™

Single-cell

FLASH-seq service

Our Single-cell FLASH-seq services deliver raw sequencing data (fastq files), gene count matrices and analysis report files, from FACS-sorted single cells. A cost-efficient option suitable for projects of all sizes.

Simply send the frozen plates to us, and we will take care of everything.

Find out more

MERCURIUS™

Low-input

FLASH-seq service

Our Low-input FLASH-seq services deliver raw sequencing data (fastq files), gene count matrices and analysis report files, from low-input samples (as low as 1 pg). A cost-efficient option suitable for projects of all sizes.

Simply send the frozen plates to us, and we will take care of everything.

FIND OUT MORE

What we say about FLASH-seq

“full-length and high-resolution single-cell transcriptomics is now accessible”

With MERCURIUS™ FLASH-seq, we are removing long-standing barriers in single-cell RNA-seq to make full-length, high-resolution transcriptomics truly accessible. Researchers studying rare cells or running high-throughput screens no longer have to compromise between sensitivity, scale, and cost. This launch is a bold step toward accelerating drug discovery and deepening our understanding of disease biology.

Riccardo Dainese, CEO and Co-founder

Featured resources

Check out our blog posts for detailed insights into the FLASH-seq technology or try our Selection Tool to find the best fit for your project.

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BLOG

12-09-2024

What is FLASH-seq?

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BLOG

27-07-2025

What is the difference between Smart-seq2, Smart-seq3, and FLASH-seq for full-length single-cell RNA-seq?

MERCURIUS™ FLASH-seq is a plate-based method that focuses on polyadenylated RNA, which includes most mRNAs. It provides detailed information on gene structure and alternative splicing. Its ability to capture full-length mRNA transcripts and detect low-abundance genes makes it a powerful tool for gene expression profiling.

FLASH-seq protocol was designed to enhance both the sensitivity and efficiency of single-cell mRNA sequencing compared to the most famous plate-based method, Smart-seq2

Read more about the technology in our blog posts: here and here.
We have significantly enhanced the original FLASH-seq method to offer a streamlined workflow and superior data output. This plate-based technology (available in 96- and 384-well formats) features a novel, non-toxic tagmentation buffer and delivers ultra-sensitive gene detection, capturing up to two times more genes compared to other commercially available solutions.
Immunology
FLASH-seq is ideal for studying rare immune cell populations, such as antigen-specific T cells or exhausted T cell subsets in chronic infections and cancer. Its high sensitivity allows researchers to capture subtle transcriptomic differences, splicing events, and even intracellular viral transcripts at the single-cell level.

Cancer
Dissect tumor heterogeneity by sequencing rare cancer stem cells or circulating tumor cells. FLASH-seq enables detection of expressed mutations, splicing isoforms, and gene fusions, providing deep insights into clonal evolution and therapeutic resistance in individual cancer cells.

Neurobiology
In complex tissues like the brain, FLASH-seq empowers researchers to analyze rare neuronal subtypes or glial cells with high resolution. It reveals alternative splicing events and single-nucleotide variants that may be critical in neurodevelopmental or neurodegenerative disorders.

Genetic Therapies & ASOs
FLASH-seq can be used to assess the impact of antisense oligonucleotides (ASOs) on target splicing at single-cell resolution. This enables precise tracking of treatment efficacy across rare or responsive cell subsets within a population.

Intracellular Pathogens
Detect intracellular viral RNA in infected cells—even when those cells are extremely rare. FLASH-seq allows you to simultaneously monitor host responses and viral transcript presence, crucial for studying latent infections or early-stage viral spread.

FLASH-seq technology

Ultra-sensitive, cost-effective and fast single-cell RNA-seq

Benefits

Applications

Cancer Research

Developmental Biology

Neuroscience

Immunology

Sub-cellular content

Genetic Therapies & ASOs

Performance

MERCURIUS™ FLASH-seq shows the highest sensitivity in gene detection​

The sensitivity of MERCURIUS™ FLASH-seq is retained even in highly heterogeneous populations​

MERCURIUS™ FLASH-seq is a full-length scRNA-seq protocol ​

MERCURIUS™ FLASH-seq shows high sensitivity for low sample inputs ​

MERCURIUS™ FLASH-seq can discriminate rare cell populations in heterogeneous samples ​

Available as kits and services

Kits for library prep

Single-cell

FLASH-seq kit

Low-input

FLASH-seq kit

Services

Single-cell

FLASH-seq service

Low-input

FLASH-seq service

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What we say about FLASH-seq

“full-length and high-resolution single-cell transcriptomics is now accessible”

Featured resources

Recent publications

FAQ

MERCURIUS™ FLASH-seq shows the highest sensitivity in gene detection

The sensitivity of MERCURIUS™ FLASH-seq is retained even in highly heterogeneous populations

MERCURIUS™ FLASH-seq is a full-length scRNA-seq protocol

MERCURIUS™ FLASH-seq shows high sensitivity for low sample inputs

MERCURIUS™ FLASH-seq can discriminate rare cell populations in heterogeneous samples