10x Genomics

High-throughput single-cell sequencing

Effortlessly analyze thousands of cells in high throughput with 10x Genomics. We offer 10x Genomics Single Cell Gene Expression, Single Cell Immune Profiling, and Single Cell Gene Expression Flex as a service.

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10x Genomics sample preparation occurs on the 10x Chromium X machine

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 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 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.

Single Cell ATAC

Single Cell ATAC-seq (scATAC-seq) provides a powerful companion to single-cell RNA profiling for a comprehensive understanding of cellular biology. While scRNA-seq reveals the genes actively transcribed in individual cells, scATAC-seq adds a layer by uncovering the accessibility of regulatory regions, enhancers, and promoters in single cells. This approach allows researchers to directly connect gene expression with chromatin accessibility.

  • Uncover the regulatory scheme of genome-wide gene expression
  • Work with a wide range of samples, the same sample requirements as for 3’ Single Cell Gene Expression and 5’ Single Cell Immune Profiling
  • With as low as 20,000 reads per nucleus, aim to target 3,000-10,000 individual nuclei
  • Combine the data with scRNA-seq to link epigenetic information (chromatin accessibility) with gene expression patterns, offering a deeper understanding of how genes are regulated and function within individual cells.

10x Genomics sequencing service

Generated your own 10x Genomics libraries and looking for a sequencing partner? With our new NovaSeq X Plus, we have a lot of capacity to sequence your 10x libraries fast. Additionally, our data team runs our 10X Genomics pipeline on your sequencing data, providing you with an exploratory data report.

Our sequencing service is also very suitable for research that requires you to have your own 10x Genomics chromium controller on site, but you are still interested in collaborating with us. Read more here.

What you can do with our 10x Genomics sequencing service
  • Sequence your 10x Genomics libraries on our NovaSeq X Plus, with unmatched turnaround times.
  • Receive raw and filtered gene count tables, Cellranger html reports and cloupe files compatible with 10X Genomics Loupe Browser.
  • For Gene Expression, Immune Profiling, and Gene Expression Flex you will also receive an exploratory downstream analysis report and a Seurat object to facilitate your own downstream analysis.

Case studies

Pioneering 10x Flex on OCT-Embedded Patient Brain Tissue

10x Genomics opened the gates for single-cell sequencing on non-fresh, non-thawed tissue with their Chromium Single Cell Gene Expression Flex (10x Flex) kit. Now, we have been successful in performing…

RNA Flex

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.

Step 1 - Consultation with our clients
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.

Meet our experts

Step 2

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. In the case of nuclei, the sample preparation depends on the project. If you are based near our lab in Utrecht, the Netherlands, it's possible to use freshly dissociated samples. Contact us to discuss this.

Sample requirementsShipping information

Single cell sequencing Illumina NovaSeq scientist places samples in the new NovaSeq X machine
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.

Sample and library QC

Step 4 - Analysis of sequencing data
Step 4

Data Analysis

Our data team performs exploratory 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.

Our data analysisView exploratory report


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 updates during processing, including QC reports.
  • Raw sequencing data (FASTQ files)
  • Raw and filtered gene count tables
  • An interactive preliminary analysis report including QC, clustering and differential gene expression analysis  
  • A Seurat object to do your own analysis with the Seurat pipeline
  • A cloupe object for easy analysis with the Loupe browser by 10x Genomics
  • 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
Information Guide 10x Genomics

10x Genomics
Information Guide

Get an overview of Single Cell Discoveries, 10x Genomics, how to get started, and more in our 10x Genomics information guide.


Recent publications using 10x Genomics

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.