Sensitive and highly versatile 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.

Learn more  Our benefits

Single-Cell Sequencing in Developmental Biology

Benefits of SORT-seq

Compatible with many sample types

SORT-seq can handle cells of all shapes and sizes. Cells normally too big for 10x Genomics (e.g., whole cardiomyocytes) can be analyzed with SORT-seq without any issues. We have experience with more than twenty species and dozens of tissue types, from patient-derived xenografts to primary tumors and from macaque brain tissue to plant stoma cells.

Focus on your region of interest

As the cells are FACS-sorted, SORT-seq can be focused on any selection of cell types that FACS can separate based on size, light scattering, or fluorescent labels.

Adaptable for low cell input

The 384-well cell-capture plates of SORT-seq make the technology suitable for as little as hundreds of cells per sample. You can perform single-cell sequencing as long as you can fill a plate with FACS sorting.

Information Guide SORT-seq

Get the Information Guide

Download our information guide to access an overview of Single Cell Discoveries, explore our single-cell sequencing services, learn how to get started, and gain more valuable insights.


Features of Sort-SEQ

Plate-based single-cell transcriptomics

SORT-seq is a single-cell RNA sequencing platform with high sensitivity and flexibility. Its cell-capture plate core and FACS compatibility enable the application to a broad range of sample types, organisms, and tissues.

Single Cell Discoveries is the exclusive provider of SORT-seq. The technology was invented by Single Cell Discoveries founder Mauro Muraro during his PhD in the Van Oudenaarden Lab. The technology was first published in 2016 and has since been cited over 700 times. You can find all published scientific studies that employ SORT-seq here.

The technology is a partially robotized version of CEL-Seq2, acclaimed in benchmark studies for its accuracy, sensitivity in identifying rare cell types, and excellent reproducibility.

You can start small with SORT-seq, sequencing, and evaluating a pilot cell-capture plate first. This makes the technology a good fit for frontier science projects. It is suitable for systematic compound screening, lead optimization, or disease model validation.

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Dr. Samuel García Pérez Galicia Sur Health Research Institute

"Fantastic job made by a really professional and friendly team. I strongly recommend Single Cell Discoveries for sequencing services."

Dr. Vanessa LaPointe MERLN Institute for Technology-Inspired Regenerative Medicine

“What we appreciate most is the nature of the collaboration. With Single Cell Discoveries, we could discuss the design of our 10x Genomics experiments, which analyses to do, and how to solve our challenges.”

We are single-cell
sequencing experts

At Single Cell Discoveries, we are 100% focused on single-cell and spatial transcriptomics. This focus enables us to take on both large-scale projects and create customized solutions for each client project. Our R&D team is actively developing novel single-cell sequencing technologies, multi-omic applications and spatial transcriptomics.

Our experience is unmatched in the field

Our team of PhD-level scientists and bioinformatics experts are at the forefront of single-cell sequencing research. We have been working in the single-cell field since 2012. Our co-founder and CEO Mauro Muraro published our SORT-seq technology, and our R&D consultant is the mind behind VASA-seq. We have experience in over 40 organisms and 30 tissues, and are able to quickly adapt workflows for novel samples.

We help you stay ahead of the curve

At Single Cell Discoveries, we are committed to continuously integrate leading-edge technologies into our service offerings to ensure clients have access to the latest advancements in single-cell genomics. Our R&D department works to both internalize the best commercial platforms and advance our own single-cell innovations to provide you with the highest quality results.

We work with you as a collaborative partner

Our team will work closely with you, providing guidance and support throughout your research journey. We are dedicated to maintaining a high-touch, collaborative relationship with clients as we scale our capacity to accommodate larger projects. By acting as your thought partner, we delve deep into the intricacies of your research and offer valuable single-cell insights.

Trusted by
The premier single-cell CRO

Accelerate your research with our tailored single-cell sequencing solutions

Located in Utrecht, the Netherlands, our purpose-built single-cell sequencing lab is operated by a team of PhD-level scientists, some of whom have pioneered the single-cell platforms we employ to deliver exceptional service. At Single Cell Discoveries, we are dedicated to crafting customized solutions for your unique challenges, ensuring rapid turnaround times, and unlocking high-impact biological insights. We eat, sleep, and breathe single-cell biology so you can focus on advancing your discovery program.

Accelerate your research with our tailored single-cell RNA sequencing solutions

How we supercharge
your research

Project Design

  • Strategize with our PhD-level account executives to decide between multiple single-cell technologies, including two exclusively offered by us.
  • Leverage our experience with 200+ clients over 1000+ unique projects.

Sample Processing

  • Run in our purpose-built single-cell lab with Illumina Novaseq X.
  • Benefit from our experience with 8500+ samples sequenced in 40+ organisms and 30+ tissue types with over 10M single cells sequenced.

Data Analysis

  • Gain quick insights into your single-cell data with our preliminary analysis report with QC, clustering, and differential gene expression.
  • Uncover biological insights through custom data analysis with our bioinformaticians who have processed over 50 terabytes of single-cell data.
Person having online consultation
Step 1


Every project starts with one or more free consultations because no two single-cell projects are the same. Our experienced PhD-level team discusses your biological question, sample type, planning, data analysis options, and other wishes. This will ensure you select the best method for your project and can hit the ground running.

Person working in hood and second person working with PCR machine
Step 2

Sample Preparation

SORT-seq is a plate-based method. You can order your SORT-seq plates with us, sort your samples into the plates, and ship them back to us.

Person loading Illumina NextSeq2000
Step 3

Processing in Our Lab

Our experienced team performs the SORT-seq protocol in our lab. We sequence the libraries on our Illumina NovaSeq X Plus or NextSeq 2000. We’ll do multiple QC checks and keep you informed of the status of your project.

Exploring data analysis
Step 4

Data Analysis

Our data consulting team is ready to assist with further guidance or tailored analysis projects such as pseudotime and gene set enrichment analysis.


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 updates during sample processing, including QC
  • Raw sequencing data (FASTQ files)
  • Gene count tables
  • QC report of mapping results (raw and mapped reads per sample, and PCA plot)
  • An explanation from our data team about data quality metrics
  • All raw sequencing data, results and reports are processed on EU servers, and securely encrypted using an AES (Advanced Encryption Standard) algorithm with a 256-bit key, before being delivered to the customers and archived.
How many plates should I sort for each sample?
We advise two plates for each sample or condition. This ensures a technical backup plate is always available in case something goes wrong with shipment or processing.
Information Guide SORT-seq

Discover our SORT-seq service

Download our information guide to access an overview of Single Cell Discoveries, explore our SORT-seq single-cell sequencing service, learn how to get started, and gain more valuable insights.