10x Genomics Single Cell Sequencing Services

We are a Certified Service Provider for 10x Genomics Single Cell Gene Expression and Single Cell Immune Profilling

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Hubrecht Institute
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High-throughput single-cell sequencing

10x Genomics provides high-throughput microfluidics-based single-cell sequencing solutions. At Single Cell Discoveries, we offer two of those solutions as a complete service: Single Cell Gene Expression and Single Cell Immune Profiling. 

Read more about these solutions below. 

Available products

The two different 10x Genomics products we offer have different applications and uses.

Single-cell Gene Expression

The Single Cell Gene Expression solution provides users with 3’ transcriptome gene expression at single-cell resolution. This allows you to perform molecular and cellular characterization of 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 cryopreserved and methanol-fixed samples  
  • Aim to target between 3,000 and 10,000 cells 
  • Choose your amount of reads per cell for the 3’ Gene Expression Library: between 30,000 and 80,000 reads per cell. 50,000 reads per cell is the most popular.
  • Compatible with single cells or nuclei* 

*Not applicable to all tissues, sample types, and projects: please contact us to discuss this option. 


Single-cell Immune Profiling

The Single Cell Gene Expression 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 and innate immune cell diversity, and 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 data and the immune repertoire 
  • Aim to target between 3,000 and 10,000 cells 
  • Choose the additional Immune Profiling Libraries: BCR, TCR and/or Cell Surface Library 
  • Choose your amount of reads per cell for the 5’ Gene Expression Library: between 30,000 and 80,000.  50,000 reads per cell is the most popular 
  • Choose your amount of reads per cell for the Immune Profiling Library: 5,000 reads per cell is recommended per Immune Profiling Library 

Certified Service Provider


  • Speed
    We are trained on 10x Genomics' best practices, to help you accelerate your research
  • Expertise
    Gain access to our team of highly trained scientists
  • Quality
    We have participated in a training and evaluation process to become a Certified Service Provider. Each year, we undergo a recertification process

How does it work?

Step 1: Sample preparation

Each 10x Genomics project starts with a consultation to aim for the best results. After this consultation, you can start with the preparation of your samples.  

Create in your own lab s single-cell suspension from your samples and ship your samples to Single Cell Discoveries on dry ice. We serve customers from all around the world. 

If you are based near our lab in Utrecht, the Netherlands, then it may be possible to use freshly dissociated samples. Please contact us to discuss the possibilities. 


Sample prep of 10x Genomics
Our Single Cell Sequencing Lab

Step 2: Sample processing and library prep

After receiving your samples, we perform quality controls to ensure that your sample is suitable for single-cell sequencing. We wash, filter and count each sample to ensure we load a high-quality cell suspension that meets the 10x requirements. 

Thereafter, the sample is loaded on the chip according to 10x Genomics specifications, along with barcoded beads and reagents. 

The chip is placed in the 10x controller, and we start the run to initialize single-cell isolation, barcoding and transcript amplification.  

After the 10x run is finished, we complete the next-generation sequencing (NGS) library preparation and send the samples out for sequencing. 

Step 3: Sequencing and data analysis

The finished NGS libraries are sent to one of our sequencing partners for NGS. After receiving the sequencing data, we map the data to the appropriate reference transcriptome and perform a QC analysis, a preliminary clustering and differential gene expression analysis. 

Mapping of sequencing data and initial quality controls are performed with the standard 10x Genomics Cell ranger pipeline. You will be provided with a cloupe data file for browsing the data with the 10x Genomics Loupe Browser.  

We will also provide you with a preliminary clustering and differential gene expression analysis, done with a customized version of the Seurat analysis pipeline.  

 In addition, we will also provide you with a license to the BBrowser offered by BioTuring, for data analysis without code. 


Data analysis VASA-seq

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Why work with us

  • Dedicated Service Provider
    We focus on high-quality (single-cell) RNA sequencing services.
  • Cost-effective Services
    Multiple scalable technologies available for every budget.
  • Personal Approach
    We like to get to know you and your project so we can aim for the best results together.
  • Expertise
    We've been running standard and out-of-the-box single-cell experiments since 2012.
  • Support
    We help you design your project and analyze your data with our (optional) data solutions.
  • Global Reach
    We serve customers all around the world.


How much does single-cell sequencing cost?

The price per sample for a 10x Genomics single-cell sequencing project depends on multiple factors and is mostly influenced by the number of samples, the number of cells per sample that you want to target, and the number of required sequencing reads per cell. Typically, pricing starts at around €3000 per sample (excluding VAT) for academic customers.

Complete the form on this page to receive an accurate estimate of your price per sample.

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Bastiaan Bijl

Head of Business Development

Questions about our 10x Genomics services? Contact us or schedule a consultation to discuss your project.

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