10x Genomics

Analyze single cells, thousands at a time

Effortlessly analyze thousands of cells with 10x Genomics. Solutions offered are 3’ Single Cell Gene Expression and 5’ Single Cell Immune Profiling.

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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 or watch our webinar with 10x Genomics here


As a Certified Service Provider, we are trained on 10x Genomics' best practices. Each year, we undergo a recertification process.

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Available products

The two 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 buying guide

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 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 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 

Key benefits of 10x Genomics

  • Analyze thousands of cells per sample
    The 10x Genomic system allows us to target thousands of cells per sample, resulting in a low cost per cell for high-throughput projects.
  • Obtain multi-dimensional single-cell data
    If you choose the 5’ Single Cell Immune Profiling solution, you can analyze the transcriptome, the T-cell and/or B-cell receptor repertoire, cell surface proteins, and antigen-specificity, all at single-cell level.
  • You’re in good company
    Currently, the 10x Genomics single-cell platform has been used in more than 1,000 peer-reviewed publications, so you are far from alone in using this technique. Whatever your biological question, chances are that 10x Genomics services will have been used on similar tissue or species.

How does it work?

Step 1: Sample preparation

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.

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

Sample prep of 10x Genomics
Our Single Cell Sequencing Lab

Step 2: Sample processing and library prep

After receiving your samples, our team carefully prepares them, either by thawing cryopreserved samples or rehydrating MeOH fixed samples.

Then we wash, filter and count each sample to ensure we load a high-quality cell suspension that meets the 10x requirements. We also verify the quality of the sample as we count.

Next, we load the cell suspension 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.

Once the 10x run is finished, we complete the NGS library preparation and send the sample out for sequencing.

Step 3: Sequencing and data analysis

We send the finished NGS libraries to one of our sequencing partners for next-generation sequencing on the Illumina NovaSeq 6000.

When we've received the sequencing data, we map it to the appropriate reference transcriptome, perform a QC analysis, a preliminary clustering and differential gene expression analysis.

Mapping of sequencing data and initial quality control reports are done with the standard 10x Genomics Cell Ranger pipeline. You'll be provided with a cloupe data file for browsing the data with the 10x Genomics Loupe Browser.

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

Data analysis VASA-seq


As with all of our services, we provide ongoing support from our single-cell sequencing specialists. For each 10x Genomics project, we provide the following:

  • Regular email updates during sample processing
  • Raw sequencing data (FASTQ files)
  • A standard Cell Ranger QC report
  • A standard Loupe Browser visualization file (cloupe)
  • Mapped count tables for downstream analysis
  • A preliminary clustering analysis, done with the Seurat pipeline.
  • A preliminary differential gene expression analysis

Once we have sent you the data, we'll invite you to schedule a call with one of our scientists to go over any additional questions you may have.

That's when we can discuss any additional data analysis you may need.

Can I use 10x Genomics?


Use our single-cell sequencing buying guide to find out if 10x Genomics Single Cell Gene Expression or Single Cell Immune Profiling matches your project.


Try our Buying Guide


How should I send you the samples?

We accept cryopreserved and methanol-fixed samples for the 3’ Single Cell Gene Expression services.

For the 5’ Single Cell Immune Profiling service, we accept cryopreserved cells.

If you are located close to our lab in Utrecht, the Netherlands, then we can discuss receiving a fresh sample as well.

related technologies

Not sure if 10x Genomics is right for your project? Explore our other services.


Highly cost-effective plate-based single-cell transcriptomics.


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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