Single-cell FLASH-seq service

Benefits

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

Full-length coverage: From differential gene expression to splicing variants and isoform detection.

No prior RNA extraction needed: Simply FACS-sort the cells in the provided plates and send them our way.

Fast turnaround times: From samples to data in as little as four weeks.

MERCURIUS^TM

FLASH-seq service

The MERCURIUS™ FLASH-seq service offers the most sensitive, full-length mRNA and cost-effective solution 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.

As part of the FLASH-seq service, clients simply need to deliver to our service centers (located in Switzerland and the United States) frozen FACS-sorted cells in our dedicated 96- or 384-well plates. The plates contain our proprietary lysis buffer for cell lysis and RNA solubilization.

Our FLASH-seq team will then process the plates and return results in as little as four weeks.

As a result of our service, our clients receive raw sequencing data (fastq files), gene count matrices and analysis reports files.

Optional downstream differential gene expression analysis is also available upon request.

How it works

Step 1

Alithea ships the plate(s)

The wells of the plate(s) contain the lysis buffer.

Step 2

Client FACS-sorts the cells and freezes the plate(s)

Single-cell FLASH-seq sample submission guidelines

Step 3

Client ships the plate(s) to Alithea

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

Sample submission form for MERCURIUSTM service

Step 4

MERCURIUS™ FLASH-seq

2 days

Step 5

Library QC - Client Checkpoint

(Fragment analyzer)

1 week

Step 6

Deep sequencing

1 week

Step 7

Data analysis and reporting - Client Checkpoint

Example of sample report

1 week

Step 8

Data

Optional: Alithea performs Differential Gene Expression analysis

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).

FAQs

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.
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 Sample Submission Guidelines for more details.

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!

Relevant publications

Explore the latest, relevant publications in the industry to learn more about our technologies.

Explore

Want to do FLASH-seq in-house?

Experience ultra-sensitive and full-length mRNA library prep kit for single-cell sequencing.

complementary kit

Benefits

FLASH-seq service

How it works

Alithea ships the plate(s)

Client FACS-sorts the cells and freezes the plate(s)

Client ships the plate(s) to Alithea

MERCURIUS™ FLASH-seq

Library QC - Client Checkpoint

Deep sequencing

Data analysis and reporting - Client Checkpoint

Data

Optional: Alithea performs Differential Gene Expression analysis​

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 ​

FAQs

Relevant publications

Want to do FLASH-seq in-house?

Speak with one of our RNA experts

Optional: Alithea performs Differential Gene Expression analysis

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