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I’ve been fortunate to combine my scientific expertise with my desire to contribute to knowledge valorization. I completed my PhD in oncology, did a post-doc in Spain, was interested in personalized medicine and genomics, and knew that I didn’t want to become a group leader. I also wondered how we, as a community, can improve the utilization of knowledge after publication: How can we keep the momentum going? And, more personally, how can I align my personal interests and ambition to contribute in a meaningful way to the greater scientific community?

So, I contacted Edwin Cuppen, who works in genomics and personalized medicine, and told him about my dilemma. He agreed to take me on, as an experiment, as a project coordinator. Today, I split my time between his group and my role as Manager of the Utrecht Sequencing Facility (USEQ). 

Our aim is to help researchers with their NGS experiments, stimulate knowledge transfer between groups, and optimize the use of our resources on the Utrecht Science Park

Are USEQ-ing help?

Genomic sequencing, also called next generation sequencing (NGS), is complex and costly. USEQ started out as a service that was provided to the local science community by Edwin’s group at the Hubrecht Institute. As the demand for sequencing grew, it became an official facility in 2014. Our aim is to help researchers with their NGS experiments, stimulate knowledge transfer between groups, and optimize the use of our resources on the Utrecht Science Park.

What’s unique about USEQ is that we’re more of a network facility. We do not own all of the infrastructure, nor is it all in one location. Rather, we have a core group of equipment and gain access to other specialized machines and expertise around the campus for users of USEQ. This maximizes our resources, is more economical (avoiding duplication of equipment purchase and maintenance) and facilitates other types of collaborations between researchers. Fees are subsidized by the UMC Utrecht, Utrecht ľ¹Ï¸£ÀûÓ°ÊÓ and Hubrecht Institute, which lowers costs by 3-fold or more (depending on the sequencing platform).

How can we help you?

We can help with the entire process: design, preparation, execution and analysis. Come to us as early as possible – even if you’ve just started thinking that maybe you’ll do an experiment. The better your experimental design, the better your results will be. Every week we hold a consulting hour on Friday afternoon. Email us [SO1] for a meeting and we’ll make sure that our full team is available: we have two full-time technicians, a bioinformatician, and a project manager (myself). In addition, colleagues from the UMCU Bioinformatics Expertise Core () attend the consult as well, and if we need additional expertise, we make sure to find the right people.

We offer different types of services along the pipeline. If you chose the full package, it would look like this: DNA or RNA isolation (max. 2 weeks), library generation (max. 3 weeks), sequencing (max. 2 weeks), for a total of 7 weeks. Of course, you can choose to prepare your own libraries and submit them to us for sequencing. You’d then have your results in about 2 weeks. We do have strict regulations on how to submit samples (purity, concentration, etc) – suboptimal samples make suboptimal data or even complete failure of the sequencing run. We also train researchers, if time allows, in some of these methods.

Come to us as early as possible – even if you’ve just started thinking that maybe you’ll do an experiment

Big data is…well, big

Sequencing produces a lot of data. A lot. To put this into perspective, our most popular machine, the Illumina NextSeq, produces roughly 350 million reads (35 gigabytes) in a run and our smaller Illumina MiniSeq machine produces 10 million reads (2.5 gigabytes). We’re hoping to gain access to a NovaSeq, which can produce a maximum of 3 terabytes of data. In addition, through our collaborators we facilitate access to Nanopore sequencing platforms for long sequencing reads, as well as to a HiSeq X Ten platform for human whole genome sequencing.

We have a fully automated workflow, and when your sequencing is finished, computational scripts check the quality of your data, before it’s sent to you. To help you handle these huge amounts of data and to analyze them properly, we work closely with the UMCU Bioinformatics Expertise Core.

The variety and flexibility I have during my daily activities is what I enjoy most and I work with many different people with various backgrounds (e.g. scientists, supporting facilities, students, lawyers and doctors). By diving deep and literally analyzing single letters of our genetic code, we’re able to help researchers paint the bigger picture of what goes wrong during disease. Together, we’re moving the field of genomics forward and doing more with the knowledge that we gain.  

Utrecht Sequencing Facility
Stratenumgebouw UMCU
Universiteitsweg 100
3584 CG Utrecht
The Netherlands
Email: useq@umcutrecht.nl