Accelerate your research

Single nuclei RNA sequencing

Imagine a world where groundbreaking discoveries are at your fingertips, where each cell holds a treasure trove of information waiting to be unlocked.

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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.

Information Guide preview: 10x Genomics

Get the Information Guide

Download our information guide to access an overview of Single Cell Discoveries, explore our 10x Genomics single-cell sequencing services, learn how to get started, and gain more valuable insights.


10x Genomics solutions

10x Genomics provides high-throughput microfluidics-based single-cell sequencing solutions. The three different 10x Genomics products we offer have different applications and uses. Find out if one of these products matches your project with our single-cell sequencing selection tool or by speaking to our experts.

Single Cell Gene Expression

The 10x Genomics Single Cell Gene Expression solution provides users with 3’ transcriptome gene expression analysis at single-cell resolution. This enables molecular and cellular characterization of individual cells. This high-throughput single-cell sequencing solution is highly suitable for larger projects that require data for a few thousand cells per sample.

What you can do with our 10x Genomics Single Cell Gene Expression service:
  • Obtain 3’ single-cell transcriptomics data from your tissue of interest;
  • Target between 3,000 and 10,000 cells and choose your amount of reads (30,000 – 80,000) per cell; the most popular option is 50,000 reads per cell.
  • Compatible with single cells or nuclei, depending on the project.


Person performing 10x Genomics experiment at Single Cell Discoveries

Single Cell Immune Profiling

The 10x Genomics Single Cell Immune Profiling solution provides users with 5’ transcriptome gene expression, combined with the T and B cell repertoire and antigen specificity. It allows you to, for example, explore the adaptive immune cell diversity or characterize the immune response to infection or treatment

What you can do with our 10x Genomics Single-Cell Immune Profiling service: 
  • Obtain 5’ single-cell transcriptomics with V(D)J T cell and B cell data
  • Target between 3,000 and 10,000 cells and choose your amount of reads (30,000 – 80,000) per cell; the most popular is 50,000 reads per cell.
  • Choose the additional Immune Profiling Libraries: BCR, TCR and/or Cell Surface Library (CITE-seq) and choose your amount of reads. 5,000 reads per cell is recommended.

Single Cell Gene Expression Flex

The Single Cell Gene Expression Flex solution enables single-cell 3’ transcriptome gene expression profiling of FFPE and fixed tissue. It allows for immediate preservation of samples on site. This is highly convenient for biopsies and patient-derived xenograft tissue, time-course experiments, sensitive cell types, and cells of lower viability. Available for mouse and human tissue.

What you can do with our 10x Genomics Single Cell Gene Expression Flex service:  
  • Obtain 3’ single-cell transcriptomics data from FFPE and paraformaldehyde-fixed samples. 
  • Aim to target up to 1,024,000 fixed single cells simultaneously with a scalable multiplexing workflow that can be run on your schedule. 
  • Choose your amount of reads per cell for the Single Cell Gene Expression Flex Library: between 10,000 and 40,000 reads per cell. Discuss with our specialists to find your option. 
  • Compatible with single cells or nuclei.

Benefits of 10x Genomics

Analyze thousands of cells per sample

The 10x Genomic system enables targeting thousands of cells simultaneously per sample, resulting in low costs per cell for high-throughput projects.

Obtain multi-dimensional single-cell data

With Single Cell Immune Profiling, you can analyze the transcriptome, T-cell and/or B-cell receptor repertoire, cell surface proteins, and antigen-specificity, all at the single-cell level.

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Dr. Bram Slütter Leiden Academic Centre for Drug Research

“It’s the expertise that Single Cell Discoveries has in single-cell and T cell receptor sequencing, even though you are flexible, that makes it preferential for us to work with an industry partner like you.”

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.”

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.

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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.

Sample preparation
Step 2

Sample Preparation

For 10x Genomics, create a single-cell suspension from your sample and either cryopreserve or methanol-fix the cells. Then, send your samples to our lab on dry ice. In the case of nuclei, the sample preparation depends on the project. 

Person loading Illumina NextSeq2000
Step 3

Processing in Our Lab

Our experienced team performs the 10x Genomics 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.

Step 4

Data Analyis

Our data team performs preliminary data analysis using a Seurat pipeline, checks the data quality and discusses irregularities with our lab team if necessary. You will receive the raw data files, data report, and guiding explanations. Talk to our data consulting team for help or request additional assessments such as pseudotime and gene set enrichment analysis.

How are projects priced?

Pricing depends on the cells per sample, sequencing depth, viability of input materials, and required protocol modifications. Your account manager can give pricing information specific to your project’s requirements during consultations.

Information Guide

Discover our 10x Genomics solutions

Download our information guide to access an overview of Single Cell Discoveries, explore our 10x Genomics single-cell sequencing services, learn how to get started, and gain more valuable insights.