MERCURIUS™

Low-Input FLASH-seq Kits

Ultra-sensitive and full-length RNA-seq technology for ultra low-input RNA samples

Library preparation kits for Illumina®, AVITI™ and Ultima Genomics sequencers.

Discover Sample Datasets

PBMCs, HEK293

Ultra-sensitive
gene detection

Full-length
transcript coverage

For rare cell populations

For precious
low-input samples

Product Overview

Built for teams requiring maximum sensitivity to detect the largest number of full-length genes possible from precious, ultra-low-input RNA samples (1 pg – 1 ng per well).

The MERCURIUS™ Low-Input FLASH-seq RNA-extraction-free protocol combines ultra-sensitive gene detection with full-length transcript coverage in a 96-well plate-based workflow. It enables ultra-low-input RNA-seq on Illumina® and AVITI™ platforms without compromising depth, data quality, or sensitivity.

of extracted RNA
From 0 pg
detected genes at
0.5M reads/sample
0 +
library prep workflow
Down to 0 day

Applications

  • Low-input RNA-seq for scarce samples (e.g. small biopsies, rare or sorted populations, limited clinical material) where standard RNA-seq kits fail.

  • Full-length mRNA sequencing of low-input RNA to profile differential gene expression, splicing variants and isoforms from precious samples at pg to ng input. 

  • Automation-friendly, plate-based transcriptome profiling for low-input studies in immunology, oncology, neuroscience and translational research where sensitivity and sample conservation are critical.

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 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.

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
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
Akisawa Satomi, Riho Saito, Tadahaya Mizuno, Hiroki Sugishita, Hideki Ukai, Shigeyuki Shichino, Masashi Yanagisawa, Kouji Matsushima, Yukiko Gotoh, Tomohiko Okazaki.
2022
Hahaut, V., Pavlinic, D., Carbone, W et al.,

Application

Full-length mRNA sequencing for low-input RNA samples

Equipment compatibility

Illumina, AVITI and Ultima Genomics instruments

Species compatibility

All eukaryotic species

Available formats

96 preps

Shipping conditions

Dry ice

Storage conditions

-20C
MERCURIUS™ Low-Input FLASH-seq is a plate-based, full-length, single-cell RNA-seq method that captures polyadenylated mRNA transcripts in ultra-low-input RNA samples. It provides detailed information on transcript isoform usage, structure, and alternative splicing.
 
Its ability to capture full-length mRNA transcripts and detect low-abundance genes makes it a powerful tool for detecting rare cell types.
 

The FLASH-seq protocol was designed to enhance both the sensitivity and efficiency of single-cell mRNA sequencing compared to other plate-based methods, like 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 96-well plate-based technology features a novel, non-toxic tagmentation buffer and delivers ultra-sensitive gene detection, capturing up to twice as many genes as 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.

The MERCURIUS™ Low-Input FLASH-seq protocol is designed for low RNA input from precious samples (1 pg to 1 ng), subcellular inputs, liquid biopsies, exosomes, microbiopsies, small organoids, and early embryos.

You are required to extract RNA from the samples and normalize them to the same concentration prior to freezing and shipping.

Please note! To preserve sample quality during shipping, plates must be placed between dry ice—not just on top. Inadequate cooling may compromise RNA integrity!

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

Ask your question:

Kit name

Catalog number
Total preps
Species compatibility

MERCURIUS™ Low-Input FLASH-seq library prep kit (96 preps)

#10931
96
Human, mouse, rat,
all eukaryotic species

Relevant blogs

August 27, 2025

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

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

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

November 5, 2024

Revolutionizing Single-Cell RNA Sequencing with FLASH-seq The field of genomics is advancing rapidly, and one of the most transformative tools has been single-cell RNA sequencing…

Interested in ordering MERCURIUS™ RNA-seq kits?