Single nuclei RNA sequencing


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Our single nuclei RNA sequencing service

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

The 10x Genomics Chromium Controller, microfluidics chip, and reagents allow you to effortlessly isolate, barcode, prepare and analyze thousands of nuclei per sample.

Single Cell Discoveries offers complete, high-quality single-cell sequencing services. For single nuclei RNA sequencing, we are able to set up custom projects.

10x genomics

Single nuclei RNA sequencing can be done with the 10x Genomics Single Cell Gene Expression solution.

This solution provides single nuclei transcriptomics data for up to 10,000 nuclei per sample, at a cost-effective price per nucleus.

It allows you to:

  • Identify the different cell types in your sample
  • Determine the heterogeneity of your sample
  • Compare sample before and after treatment at high resolution

Single nuclei RNA sequencing

Single nuclei RNA sequencing is performed on cells that are difficult to isolate, as an alternative for single-cell sequencing. Instead of using individual cells, the nuclei are isolated and loaded onto the 10x Genomics Chromium Controller.

The most important difference of single nuclei RNA sequencing compared to single-cell sequencing is the protocol.

Because we have to isolate the nuclei first, the labwork is a bit more challenging. A single nuclei RNA sequencing project will therefore be customized to match your tissue type.


Why work with us

  • Dedicated service provider
    With our focus on single-cell sequencing only, we are the one-stop-shop for all your single-cell sequencing projects.
  • Continued support
    We make sure to provide continuous support, even after we have sent you the results from your experiment.
  • Cost-effective services
    We work with you and your budget to make sure you don't have to break the bank.
  • Expert team
    We have been running single-cell experiments since 2012, and have published in numerous high-impact journals
  • Short turnaround times
    From receipt of the samples, you can expect results in 4 - 6 weeks.
  • Based in Europe
    Your samples are processed and sequenced in Europe (Netherlands & UK)

How does it work?

Step 1: Sample preparation

For some tissue types, we can isolate nuclei from frozen tissue.

In that case, you can send us the frozen tissue so we can perform the nuclei isolation.

To find out if we can help you with the nuclei isolation, please book a consultation with one of our specialists. In that meeting, we can discuss your tissue type and experimental setup.

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Sample prep of 10x Genomics
Our Single Cell Sequencing Lab

Step 2: Sample processing and library prep

After receiving your samples, we carefully check your samples and proceed with the library prep according to the 10x Genomics protocol.

Once we finish the library prep, we send the NGS libraries to one of our sequencing partners for sequencing.

Step 3: Sequencing and data analysis

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

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

Finally, we provide you with the raw sequencing data, as well as the results of the QC and the preliminary analysis, so you can start with analyzing your data straight away.

Data analysis VASA-seq


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

  • Regular email updates during sample processing
  • Raw sequencing data (FASTQ files)
  • A QC report
  • A standard Loupe Browser visualization file
  • 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.

Schedule a meeting

Schedule a consultation with one of our specialists to discuss your options.


Bastiaan Bijl

Head of Business Development

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