Full-length, total RNA single-cell sequencing

VASA-seq is a brand-new technology for full-length, total RNA sequencing at single-cell level. Exclusively offered as a service by Single Cell Discoveries.

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*VASA-seq 1.1. will be launched in May 2023. The current VASA-seq protocol will be discontinued shortly. Read more about VASA-seq 1.1.

Full-length, total RNA, single-cell transcriptomics

VASA-seq is a single-cell sequencing platform for full-length, total RNA sequencing.

As with SORT-seq, VASA-seq is based on 384-well cell capture plates and flow cytometry (FACS) sorting.

However, unlike other single-cell sequencing technologies, VASA-seq does not rely on primers that bind to the endogenous poly-A tail of mRNA molecules.

This means that VASA-seq allows us to analyze non-coding RNA species and immature mRNA molecules simultaneously, all at single-cell level.

Currently, VASA-seq is only compatible with human, mouse or rat samples.

Briefly, this is how it works: We receive your single cells, sorted into the wells of a prepared 384-well cell capture plate.

Then, RNA molecules are barcoded with primers that contain a cell-specific barcode.

After barcoding, double-stranded cDNA is generated, then we pool the contents of the wells and start the amplification of the RNA with in-vitro transcription (IVT).

Once IVT is complete, we prepare the sample into an Illumina sequencing library.

Read more about how VASA-seq works in this publication.

What you can do with VASA-seq

VASA-seq is highly suited to single nucleus sequencing, since it does not depend on polyadenylation and can capture the immature RNA molecules in the nuclei that have not yet developed a poly-A tail.

Also, you can use VASA-seq to sequence total RNA to study non-coding RNA species such as long non-coding RNAs and rRNAs, at single-cell level.

Lastly, because VASA-seq generates full-length information on the RNA molecules, you can study RNA isoforms at single-cell level.

VASA-seq provides the ideal data to infer RNA velocity within your dataset as it can be used to separate reads coming from introns or exons along the full length of the RNA molecule.

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Key benefits of VASA-seq

  • Analyze RNA molecules at full length
    VASA-seq generates full-length coverage of the RNA, all the way from the 5' to the 3' end. This means you get information on intron/exon boundaries and SNPs.
  • Analyze coding and non-coding RNA species
    VASA-seq is able to sequence non-polyadenylated RNAs. This includes immature mRNAs and non-coding RNAs.
  • Compatible with all sample types
    VASA-seq works with relatively low numbers of cells. If you can fill (at least part of) a 384-well plate by FACS sorting, you can generate single-cell sequencing libraries.

How does it work

Step 1: FACS sorting

Begin by ordering our cell capture plates, which we ship worldwide. You then sort your single-cells into the 384-well cell-capture plates and send the plates back to us for processing. If you don't want us to process all the plates at once, just let us know which ones to start with.

FACS sorting

Step 2: Plate processing

Once we've received your plates, we'll process them using the VASA-seq protocol. After barcoding the mRNA of your single-cells, we'll pool the material from one plate to generate one sequencing library per plate.

Step 3: Sequencing and data analysis

We'll send the sequencing libraries to one of our partners for sequencing. When we get the data back, we'll perform a preliminary data analysis, then send the data back to you.

Data analysis of VASA-seq


As with all of our services, we provide ongoing support from our single-cell sequencing specialists. We provide the following for each VASA-seq project:

  • Regular email updates during plate processing
  • Raw sequencing data (FASTQ files)
  • A QC report per plate
  • Mapped count tables for downstream analysis
  • A preliminary clustering analysis, done with the Seurat pipeline.
  • A preliminary differential gene expression analysis

Once we have sent you the data, we'll invite you to schedule a call with one of our scientists to go over any additional questions you may have.

That's when we can discuss any additional data analysis you may need.

Can I use VASA-seq?


Use our single-cell sequencing buying guide to find out if VASA-seq matches your project.

Try our Buying Guide


Which species is VASA-seq compatible with?

Currently, VASA-seq works on cells of human, mouse and rat origin.

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Bastiaan Bijl

Head of Business Development

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