Versatile and highly-controlled single-cell transcriptomics

SORT-seq is a state-of-the-art single-cell transcriptomics technology based on FACS sorting and 384-well plates. Exclusively offered by Single Cell Discoveries.

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Trusted by
Hubrecht Institute

Plate-based single-cell transcriptomics

SORT-seq is a single-cell sequencing platform first published in 2016 by Muraro et al. and has since been cited over 700 times. SORT-seq is a partially robotized version of the lauded CEL-seq2 protocol.

See the publications that use SORT-seq here.

SORT-seq uses FACS to sort single cells into the wells of a 384-well cell-capture plate. Each well in the plate contains barcoded primers and other reagents. After barcoding, double-stranded cDNA is generated. Then we pool the contents of all wells, amplify the RNA, and prepare the sample into an Illumina sequencing library.

This sorting step makes it possible to analyze live single cells, population of interest, and cells too large for the 10x Genomics platform.

What you can do with SORT-seq

SORT-seq's flexible plate-based system makes it possible to screen small numbers of cells from many different samples without skyrocketing costs.

By combining single-cell flow cytometry data with transcriptomics data with strategies like GateID, we can find novel FACS gating strategies for desired cell types.


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Key benefits of SORT-seq

  • Modular and flexible due to the use of plates
    Working with plates allows you to start small and upscale later. We can start by processing and sequencing one plate per condition. Once the data from the first plate looks good, we can go on to process the rest of the plates. This provides you with tremendous flexibility in scaling up your experiments.
  • Compatible with all sample types
    SORT-seq works even with rare or low quantities of cells. As long as you can fill at least part of a plate with FACS sorting, you can generate single-cell sequencing libraries. Also, SORT-seq can handle cells of all sizes. Cells that are too big for the 10x Genomics system (e.g. cardiomyocytes) can be analyzed with SORT-seq without any issues.


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
Plate processing

Step 2: Plate processing

Once we've received your plates, we'll process them using the SORT-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

"The service of Single Cell Discoveries guarantees a smooth process between customer and company. In case of problems or questions, the scientists reacted competently and immediately, so that answers could be found quickly and flexibly. The staff is very friendly in dealing with the customer. Many thanks for the great cooperation."

Prof. Dr. Stella Autenrieth & Susanne Pfrommer
German Cancer Research Center


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

  • Regular email updates during plate processing
  • Raw sequencing data (FASTQ files)
  • A QC report per plate
  • Mapped count tables for downstream analysis
  • Preliminary clustering analysis with the Seurat pipeline.
  • Preliminary differential gene expression analysis
  • A follow-up meeting to discuss your questions and further data analysis needs


view preliminary report

Can I use SORT-seq?


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

Try our Buying Guide

Succes stories

Learn more about the results from our services - from a client perspective.

Champalimaud Foundation

Colorectal Zebrafish Xenograft Model

Champalimaud Foundation | This research, conducted at the Champalimaud Foundation in Lisbon, is focused on the immune response after implantation of human cancer cells in zebrafish. The cells in the implanted tumors were characterized using SORT-seq. Here, we explain how SORT-seq contributed to this remarkable study. Cancer immunoediting is a process in which the immune…

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related technologies

Not sure if SORT-seq is right for your project? Explore our other services.

10x Genomics

High-throughput single-cell gene expression or single-cell immune profiling analysis.


Full-length, total RNA single-cell sequencing platform.

bulk RNA sequencing

Don't need single-cells? Try our highly cost-effective bulk RNA seq services.

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Bastiaan Bijl

Head of Business Development

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