Single-Cell FLASH-seq Kits
for high-sensitivity full-length single-cell RNA-seq
Ultra-sensitive, plate-based single-cell RNA-seq library preparation for FACS-sorted cells, with full-length mRNA transcript coverage for rare cell detection, isoform analysis, and alternative splicing studies.
Discover Sample Datasets
PBMCs, HEK293
Ultra-sensitive gene detection
For rare cell populations
Full-length transcript coverage
Automation-ready plate-based workflow
Product Overview
Full-length single-cell RNA-seq is useful when gene-level expression alone is not enough. Compared with 3′ or 5′ counting approaches, full-length methods provide broader transcript coverage, helping researchers study isoform diversity, alternative splicing, gene-body coverage, expressed variants, fusion transcripts, and low-abundance genes in individual cells.
MERCURIUS™ Single-Cell FLASH-seq brings this full-length readout into an automation-friendly 96- or 384-well plate-based workflow for sorted cells.
at 0.5M reads/sample
Applications for full-length single-cell RNA-seq
- Rare cell population profiling
Study FACS-sorted rare cell populations with high-sensitivity single-cell gene detection. - Immunology and immune cell states
Profile antigen-specific T cells, exhausted T cells, rare immune subsets, and heterogeneous PBMC populations. - Cancer and tumor heterogeneity
Analyze rare tumor subpopulations, circulating tumor cells, cancer stem cells, fusion transcripts, and therapy-resistant cell states. - Neuroscience and developmental biology
Characterize rare neuronal or glial subtypes where transcript coverage and sensitivity are important. - Isoform and alternative splicing analysis
Use full-length transcript coverage to study transcript structure beyond 3′/5′ gene counting. - Low-abundance transcript detection
Capture weak but biologically meaningful signals in single cells with limited RNA content.
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
Sample Datasets
PBMCs
96
10'000 reads
To have access to the deep-sequenced dataset (9.5M reads per sample) contact us.
79.9 MB
HEK293
191
250'000 reads
4.9 GiB
Product documentation
User guide
Publications
- FLASH-seq, Single-cell FLASH-seq
Andrea Salati, Yves Paychère, Vincent Hahaut, Cédric Gobet, Felix Naef
- FLASH-seq, Single-cell FLASH-seq
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.
- FLASH-seq, Single-cell FLASH-seq
Akisawa Satomi, Riho Saito, Tadahaya Mizuno, Hiroki Sugishita, Hideki Ukai, Shigeyuki Shichino, Masashi Yanagisawa, Kouji Matsushima, Yukiko Gotoh, Tomohiko Okazaki.
Application
Equipment compatibility
Species compatibility
Available formats
Shipping conditions
Storage conditions
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?
How is FLASH-seq different from Smart-seq2 and Smart-seq3?
FLASH-seq is a plate-based full-length single-cell RNA-seq method designed to improve sensitivity, consistency, and workflow efficiency compared with earlier full-length scRNA-seq methods.
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?
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.
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.
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.
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?
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.
What is a full-length single-cell RNA-seq kit?
A full-length single-cell RNA-seq kit prepares sequencing libraries from individual cells while preserving transcript coverage across the gene body, enabling analysis beyond 3′ or 5′ gene counting.
When should I choose FLASH-seq instead of droplet-based scRNA-seq?
Choose FLASH-seq when your study requires high sensitivity, sorted-cell control, rare cell analysis, isoform information, alternative splicing analysis, or full-length transcript coverage. Droplet-based methods are often better when the main goal is to profile very large numbers of cells.
Ask your question:
Kit Name
MERCURIUS™ Single Cell FLASH-seq library prep kit (96 preps)
all eukaryotic species
MERCURIUS™ Single Cell FLASH-seq library prep kit (384 preps)
all eukaryotic species
Accessories
Product
Number of Samples
MERCURIUS™ Cell lysis module
MERCURIUS™ Cell lysis module
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