Single-Cell FLASH-seq Kits
for high-sensitivity single-cell RNA-seq

Q: What are the main applications of MERCURIUS™ FLASH-seq?

ImmunologyFLASH-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.CancerDissect 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.NeurobiologyIn 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 & ASOsFLASH-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 PathogensDetect 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.

Ultra-sensitive, full-length, and plate-based single-cell RNA-seq technology for sorted cells

Library preparation kits for Illumina® and AVITI™ sequencers.

Discover Sample Datasets

PBMCs, HEK293

Ultra-sensitive gene detection

For rare cell populations

Full-length transcript coverage

Automation-ready plate-based workflow

Product Overview

Built for teams requiring maximum scalability and sensitivity to detect the largest number of full-length genes possible from sorted single cells.

MERCURIUS™ Single-Cell FLASH-seq delivers ultra-sensitive full-length single-cell RNA sequencing (scRNA-seq) in an RNA-extraction-free 96- or 384-well plate-based workflow suitable for automation. Designed for maximum sensitivity, the technology detects ~2× more genes than other commercial solutions in a rapid one-day workflow. It enables sensitive, scalable scRNA-seq compatible with Illumina® and AVITI™ platforms.

extraction steps needed

Down to 0 RNA

preps in a single tube

Up to 0

genes detected
at 0.5M reads/sample

0 +

library prep workflow

Down to 0 day

Applications

High-resolution single-cell RNA-seq for differential gene expression, rare cell detection and cell type discovery in heterogeneous samples (e.g. PBMCs, tumors).
Full-length scRNA-seq for alternative splicing, isoform diversity, gene-body coverage and fusion transcript detection that 3’/5’ methods miss.
Plate-based single-cell transcriptomics on sorted cells (96- and 384-well plates), ideal for immunology, cancer, neuroscience and developmental biology projects that require ultra-sensitive, full-length readouts.

MERCURIUS™ FLASH-seq Detects More Genes Than Smart-seq3 and Smart-seq2 with Greater Consistency

FLASH-seq detects a median of approximately 11,000 genes per sample in HEK293T cells, outperforming Smart-seq3 and Smart-seq2 after downsampling all to 500k reads/sample.

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 Can Discriminate Rare Cell Populations In Heterogeneous Samples

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

Sample Datasets

PBMCs

Number of samples:
96

Reads per sample in demo dataset:
10'000 reads

To have access to the deep-sequenced dataset (9.5M reads per sample) contact us.

Demo dataset file size:
79.9 MB

HEK293

Number of samples:
191

Reads per sample in demo dataset:
250'000 reads

Demo dataset file size:
4.9 GiB

Product documentation

User guide

Publications

2025

FLASH-seq, Single-cell FLASH-seq

Molecular determinants of brain-resident CD8+ T cell formation and function.

Tarek Elmzzahi, Chun-Hsi Su, Mehrnoush Hadaddzadeh Shakiba, Doaa Hamada, DaryaMalko, Maren Koehne, Aleksej Frolov, Teisha Mason, Yuanfang Li, Rebekka Scholz, Collins Osei-Sarpong, Leonie Heyden, Jonas Schulte-Schrepping, Lorenzo Bonaguro, Kristian Haendler, Vassiliki Boussiotis, Annett Halle, Elena De Domenico, Daniel HDGray, Martin Fuhrmann, Zeinab Abdullah, Axel Kallies, Kevin Man, Marc D. Beyer.

2025

FLASH-seq, Single-cell FLASH-seq

Local niche-derived immunosuppressive CXCR2+ cells impair antiviral immunity.

Akisawa Satomi, Riho Saito, Tadahaya Mizuno, Hiroki Sugishita, Hideki Ukai, Shigeyuki Shichino, Masashi Yanagisawa, Kouji Matsushima, Yukiko Gotoh, Tomohiko Okazaki.

2022

FLASH-seq, Single-cell FLASH-seq

Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.

Hahaut, V., Pavlinic, D., Carbone, W et al.,

Application

full-length mRNA sequencing for single-cell

Equipment compatibility

Illumina, AVITI and Ultima Genomics instruments

Species compatibility

All eukaryotic species

Available formats

96 and 384 preps

Shipping conditions

Dry ice

Storage conditions

-20C

We do not recommend very large cells, such as cardiomyocytes, or any other cell type incompatible with the FACS sorting step.

What is MERCURIUS™ FLASH-seq, and how does it work?

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.

How is MERCURIUS™ FLASH-seq different than the original FLASH-seq protocol?

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.

What are the main applications of MERCURIUS™ FLASH-seq?

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.

What type of samples can be used in MERCURIUS™ FLASH-seq?

The MERCURIUS™ FLASH-seq protocol is fully compatible with whole FACS-sorted cells.

We do not recommend very large cells, such as the cardiomyocytes, as they are not compatible with the FACS sorting step.

How should I prepare the cells?

For optimal results, we require the cells to be directly FACS-sorted in the dedicated well plates. The 96- and 384-plates contain the lysis buffer. It is important for the user to sort the cells in the middle of the well. Please refer to the User Guide and the Sample Submission Guidelines for more details.

What is the sequencing depth recommended for MERCURIUS™ FLASH-seq?

The average recommended sequencing depth is 250’000 reads/cell.

Ask your question:

Kit Name

Catalog number

Total preps

Species compatibility

MERCURIUS™ Single Cell FLASH-seq library prep kit (96 preps)

#10921

Human, mouse, rat,
all eukaryotic species

MERCURIUS™ Single Cell FLASH-seq library prep kit (384 preps)

#10923

384

Human, mouse, rat,
all eukaryotic species

Accessories

Product

Catalog number

Number of Samples

MERCURIUS™ Cell lysis module

#10351

MERCURIUS™ Cell lysis module

#10352

384

Relevant blogs

August 27, 2025

MERCURIUS™ FLASH-seq vs 10x Genomics Chromium: Which Single-Cell RNA-seq Approach is Right for You?

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to examine the cellular heterogeneity of complex samples, identify new cell types, and explore transcriptional regulation at…

July 28, 2025

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

The Smart-seq2 protocol was the gold standard for full-length plate-based single-cell RNA-seq, offering superior sensitivity and the transcript coverage necessary to detect splice isoforms, allelic…

June 19, 2025

Alithea Genomics Announces the Launch of MERCURIUS™ FLASH-seq: A Plate-Based, Full-Length Single Cell RNA-seq Kit Delivering Exceptional Sensitivity and Simplicity

Lausanne, Switzerland and Frederick, MD – June 19, 2025 – Alithea Genomics, a pioneering biotech company based in Switzerland and the USA specializing in high-throughput…

DRUG-seq kits

Total DRUG-seq kits

Single-cell FLASH-seq kits

Spheroid DRUG-seq kits

BRB-seq kits

Total BRB-seq kits

Full-Length BRB-seq kits

Low-input FLASH-seq kits

High-Sensitivity BRB-seq kits

DRUG-seq service

Total DRUG-seq service

Single-cell FLASH-seq service

Spheroid DRUG-seq service

BRB-seq service

Total BRB-seq service

Full-length BRB-seq service

Low-input FLASH-seq service

High-Sensitivity BRB-seq service

Blood BRB-seq service

Total Blood BRB-seq service

Single-Cell FLASH-seq Kits for high-sensitivity single-cell RNA-seq

Ultra-sensitive, full-length, and plate-based single-cell RNA-seq technology for sorted cells

Ultra-sensitive gene detection

For rare cell populations

Full-length transcript coverage

Automation-ready plate-based workflow

Product Overview

Applications

MERCURIUS™ FLASH-seq Detects More Genes Than Smart-seq3 and Smart-seq2 with Greater Consistency

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 Can Discriminate Rare Cell Populations In Heterogeneous Samples ​

Sample Datasets

PBMCs

HEK293

Product documentation​

User guide

Publications

Molecular determinants of brain-resident CD8+ T cell formation and function.

Local niche-derived immunosuppressive CXCR2+ cells impair antiviral immunity.

Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.

Application

Equipment compatibility

Species compatibility

Available formats

Shipping conditions

Storage conditions

Ask your question:

Kit Name

MERCURIUS™ Single Cell FLASH-seq library prep kit (96 preps)

MERCURIUS™ Single Cell FLASH-seq library prep kit (384 preps)

Accessories

Relevant blogs

August 27, 2025

MERCURIUS™ FLASH-seq vs 10x Genomics Chromium: Which Single-Cell RNA-seq Approach is Right for You?

July 28, 2025

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

June 19, 2025

Alithea Genomics Announces the Launch of MERCURIUS™ FLASH-seq: A Plate-Based, Full-Length Single Cell RNA-seq Kit Delivering Exceptional Sensitivity and Simplicity

Interested in ordering MERCURIUS™ RNA-seq kits?

Single-Cell FLASH-seq Kits
for high-sensitivity single-cell RNA-seq

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 Can Discriminate Rare Cell Populations In Heterogeneous Samples

Product documentation

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