10x Genomics

Analyze single cells, thousands at a time

Analyze thousands of single cells per sample, effortlessly. Available 10x Genomics services are the 3’ Single Cell Gene Expression and 5’ Single Cell Immune Profiling products.

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Hubrecht Institute
Bergen University
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High-throughput single-cell sequencing

10x Genomics offers a complete solution for high-throughput single-cell sequencing.

With the 10x Genomics Chromium Controller, microfluidics chip and reagents, you can isolate, barcode, prepare, and analyze thousands of cells per sample, effortlessly.

At Single Cell Discoveries, we offer complete, high-quality services for the 10x Genomics Single Cell Gene Expression and the Single Cell Immune Profiling solutions.


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Available products

Single-cell Gene Expression

With the 10x Genomics Single Cell Gene Expression solution, you’ll obtain single-cell transcriptomics data for up to 10,000 cells per sample, for a cost-effective price per cell.

Here’s what you can do:

  • Identify the different cell types in your sample
  • Determine the heterogeneity of your sample
  • Find new cell-surface markers or other cell-specific targets
  • Assess immune activation as a result of adding a compound to your cells
  • Compare sample before and after treatment at high resolution

Single-cell Immune Profiling

With the 10x Genomics Single Cell Immune Profiling solution, you’ll obtain both immune repertoire and gene expression data at single-cell level for up to 10,000 cells per sample.

Additionally, you can analyze cell surface proteins and antigen specificity, all in the same experiment, to obtain multi-dimensional data on your samples.

Here’s what you can do:

  • Reveal immune cell clonality, diversity, antigen specificity, and cellular context
  • Characterize individual T-cells and B-cells
  • Identify V(D)J gene sequences
  • Pair α and β chain TCR sequences from individual T-cells
  • Pair heavy and light chain immunoglobulin sequences from individual B-cells
  • Simultaneously measure TCR, B cell Ig, cell surface protein expression, antigen specificity, and 5’ gene expression

Key benefits of 10x Genomics

  • Analyze thousands of cells per sample
    With the 10x Genomic system, we can 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.
  • Well-published/You’re in good company
    Currently, there are over a 1,000 peer-reviewed publications with the 10x Genomics single-cell platform. This means that you are far from alone using this technique. Changes are that you will be able to find publications or using 10x Genomics on similar tissue or species.

How does it work?

Step 1: Sample preparation

Create a single-cell suspension from your sample and cryopreserve or methanol-fix the cells. After this, send your samples to our lab on dry ice.

Are you located near our lab in Utrecht, the Netherlands? Then you can contact us to discuss using freshly dissociated samples.


Step 2: Sample processing and library prep

After receiving your samples, our team carefully thaws (cryopreserved) or rehydrates (MeOH fixed) the samples. To ensure we load a high-quality cell suspension that meets the 10X requirements, we wash, filter, and count each sample. During the counting, we verify the quality of the sample. Subsequently, we load the cell suspension on the chip according to 10x Genomics specifications, together with barcoded beads and reagents. The chip is placed in the 10X controller and the run is started to initialize single-cell isolation, barcoding, and transcript amplification. After the 10X run is finished, we complete the NGS library preparation and send the sample out for sequencing.

Step 3: Sequencing and data analysis

The finished NGS libraries are sent to one of our sequencing partners for next-generation sequencing on the Illumina NovaSeq 6000. After receipt of the sequencing data, we map the data to the appropriate reference transcriptome, and perform a QC analysis and 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. A cloupe data object will be provided for browsing the data with the 10x Genomics Loupe Browser.

On top of that, we provide you with a preliminary clustering and differential gene expression analysis, done with a customized version of the Seurat analysis pipeline.


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.


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.

That depends on your biological question and sample type. Typically, our customers target between 3,000 and 8,000 cells per sample. Schedule a call with one of our specialists to discuss your specific project.

That depends on your biological question. Typically, we recommend a sequencing depth between 30,000 and 70,000 reads per cell for 10x Genomics projects. Schedule a call with one of our specialists to discuss your options.

Ideally, we require a cell suspension with at least 0.5 million cells per sample. If you are unable to achieve that, please contact us to discuss the possibilities.

Yes, before you send us your sample, you can perform a FACS sort to enrich for your cell type of interest. Please bear in mind that we need enough cells to start with (see previous question).

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.

Download pricing

Ready to proceed? Use the form below to download pricing information on our single-cell sequencing services.

Bastiaan Bijl

Business Development Manager

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