Which single-cell RNA sequencing technology should I use?

Which single-cell RNA sequencing technology should I use?

There are several different technologies to choose from in single-cell sequencing projects. But which one is right to answer your biological question?

The answer to this depends on your project. Different biological questions and hypotheses may require different approaches, and therefore, a different technological solution.

This post explains the most significant technologies, their benefits, and how they compare to each other.

Do you need advice on which technology best fits your project? Try our single-cell sequencing buying guide.



SORT-seq is a cost-effective single-cell sequencing technology based on FACS sorting and 384-well cell-capture plates.

You start by FACS sorting a single live cell into each of the wells of the cell capture plate, which contains well-specific, barcoded primers. Once sorted, you freeze the plates and send them back to us for library prep and sequencing.

Key advantages of SORT-seq

  • Accessibility: with prices that start just above €1000 per sample, SORT-seq is one of the most accessible single-cell sequencing methods available.
  • Flexible: due to the modular nature of working with plates, you can start small and scale your experiment later if needed.
  • Specific: because of the FACS sorting step, you have full control of the cell type you sort into the plates. Everything is possible, from a basic unbiased sort to a very complex and specific one.
  • Handle large cell types: Some cells are so large that other single-cell sequencing platforms struggle with their size. With SORT-seq, larger cell types such as cardiomyocytes can be analyzed without issues.
  • Handle small sample sizes: You can start with as little as a few thousand cells to perform a single-cell sequencing analysis. This is useful if you don’t have millions of cells to spare.

Since its publication in 2016, SORT-seq has been applied to many different organisms and tissue types and provides a highly cost-effective and flexible alternative to other single-cell sequencing platforms.

For more information, see our SORT-seq page.



VASA-seq is also based on FACS sorting and 384-well plates. It is a new (and as yet unpublished) technology that does not rely on the presence of a poly-A tail, which means VASA-seq allows for full-length and total RNA single-cell sequencing.

VASA-seq also provides full-length sequencing information on both coding and non-coding RNA species.

The process on your side is similar to that of SORT-seq: sort your single-cells into the wells of our 384-well cell capture plates, ship them back to us, and we’ll take care of the rest.

Key advantages of VASA-seq

Full-length sequence information: You can obtain information on the entire length of the RNA molecules to analyze sequence variation such as SNVs and splice variants, all at single-cell resolution.

Non-coding RNA species:  You can analyze the total RNA contents of each individual cell by looking at non-coding RNA species such as snoRNAs, snRNA and scaRNAs.

Analyze immature mRNA molecules: when single nucleus sequencing is the only option, VASA-seq generates better data because of its ability to prime immature mRNA molecules that are yet to develop a poly-A tail.

For more information, see our VASA-seq page.


10x Genomics

10x Genomics designs and designs and manufactures devices and reagents for single-cell sequencing. Their most important product is the Chromium Controller, a microfluidics device that enables high-throughput single-cell sequencing for thousands of cells at a time.

10x Genomics is currently the market leader in the single-cell sequencing field and offers various single-cell sequencing solutions.

At Single Cell Discoveries, we offer two of their products as a service: Single Cell Gene Expression and Single Cell Immune Profiling.

Single Cell Gene Expression

With the Single Cell Gene Expression solution, we generate 3’ single-cell transcriptomics data for up to 10,000 cells per lane or sample. If you require analysis of up to 10,000 cells per sample for your experiment, the 10x Genomics platform provides a cost-effective high-throughput solution. With 10x Flex, you can study frozen and formaldehyde-fixed tissue of human and mouse origin.

Single Cell Immune Profiling

The 10x Genomics Single Cell Immune Profiling solution allows you to kill two birds with one stone. As well as obtaining single-cell transcriptomics data at single-cell level, you can also characterize the immune repertoire from the T-cell or B-cell receptors – again at single-cell level.

This means that you can measure the diversity in your immune cells and their response to a pathogen or drug with great accuracy.

Key advantages of 10x Genomics

  1. High-throughput: the 10x Genomics platform enables the analysis of thousands of cells per sample, at a low cost per cell.
  2. Well published: Currently, the 10x Genomics single-cell platform has been used in more than 1,000 peer-reviewed publications, which means that you are not alone.
  3. Standardized: Because the 10x Genomics system is commercially available, it is highly standardized, which means that consistent results are easy to obtain.

For more information, see our 10x Genomics page.


Which technology should I use?

Use our single-cell sequencing buying guide to find out which technology fits your project.

Ready to proceed? Use the form below to download pricing information on our services.