Opening up the (epi)genome of single cells

To help researchers explore both the genome and some layers of the epigenome, the facility currently offers four different technologies. Each technology helps to reveal different aspects of the (epi)genome on a single-cell level.


Whole genome sequencing

Identify genetic mutations by profiling hundreds of single cells in parallel and discover the underlying cause of cellular malfunctioning.

  1. Detect SNVs within single cells
  2. Low-cost WGS
  3. Range of coverage for different applications
About scNlaIII-seq


Identify copy number variations (CNVs) within a chromosome or at the whole chromosome level (aneuploidy) in the genome by profiling hundreds of single cells in parallel and discover the underlying cause of cellular malfunctioning.

  1. Discover CNVs as small as 2 Mbs per cell
  2. Assess the aneuploidy of your sample
  3. Low-cost karyotyping
About scKaryo-seq

Chromatin profiling

Look at the specific epigenetic factors influencing DNA-protein binding to regulate gene expression.

  1. Low number of input cells required compared to ChIP-seq
  2. Readily available for key driver histone modifications
  3. Including in-house cell sorting
About scChIC-seq

Single-cell data analysis

Need help with your data analysis, statistics or figure design? Let Single-Cell Core link you to a highly trained bioinformatician.

About Single-cell data analysis

Bulk DNA sequencing

Bulk DNA sequencing is the standard tool to generate (epi)genomic data at cell population level.

  1. More powerful and cost-effective compared to scDNA-seq
  2. Low number of 100 input cells required
  3. Can be applied to all our available techiques
About Bulk-seq

The fast and reliable production of high-quality single-cell libraries by Single-Cell Core, combined with their approachability, really helps us to bring our research projects to the next level

Van Boxtel group, PostDoc

Prinses Máxima Centrum, Utrecht, The Netherlands

How we work

Below you can see an overview of our general workflow. The sequencing time highly varies depending on the number of samples we are processing at that time.


Place order

After you have placed your order, we will send the plates to your institute

1 week

Sort single cells

You will sort the cells into the provided plates and send them back to SCC



Your samples will be processed using our state-of-the-art techniques

4 weeks


The generated libraries will be sequenced

3 weeks


The generated data will be analyzed by a bioinformatician upon your request