In this edition of Under the Microscope, we explore the cutting-edge capabilities of Newcastle University’s Genomics Core Facility (GCF) with its manager, Jonathan Coxhead. Jon walks us through the world-class sequencing services available to support diagnostic development and commercial partnerships.

Jon, can you tell us about your background and role?

I lead the Genomics Core Facility at Newcastle University. At heart, I’m a scientist who thrives in the lab, but my role also involves managing and facilitating projects—keeping me closely connected to breakthrough research.

My expertise spans cancer biology and advanced genomics technologies, particularly massively parallel sequencing and its diverse applications.

Over the past 20 years, I’ve worked in commercial, diagnostic, and research sectors, allowing me to bridge the gap between academia and industry.

Tell me about the Genomics Core Facility

Established in 2015 with investment from the MRC and Newcastle University, the GCF is a leading next-generation sequencing (NGS) hub. We specialize in single-cell and spatial transcriptomics, operating from state-of-the-art, controlled labs in the Bioscience Building at the Centre for Life.

Our capabilities include:

• Short-read sequencing (Illumina)
• Long-read sequencing (Oxford Nanopore Technologies)
• Certified Service Provider (CSP) for 10X Genomics
• Certified ‘NGS ProLab’ for Twist Biosciences

At the core of our success is a highly skilled team of five experts, dedicated to supporting world-class genomics research across academia and industry.

What Services Does the GCF Offer?

We offer cutting-edge massively parallel sequencing services, helping to decode the genome, epigenome, and transcriptome across multiple biological applications.

What sets us apart?

• Scalability – From large-scale clinical trials to niche experimental projects, we adapt to your needs.
• Versatility – We work across species and sample types, delivering both macro and single-cell solutions.
• Innovation-First Approach – We proactively develop new applications ahead of demand, ensuring cost-effective and optimized solutions for our customers.
• Problem-Solving Expertise – We’re experienced in handling compromised samples, providing robust sequencing options even when starting materials are suboptimal.

Currently, our most in-demand services include Single-Cell and Spatial Transcriptomics, driven by our pioneering SpaRTAN (Spatially Resolved Transcriptomics at Newcastle) initiative.

Can you give me some examples of specific projects you’ve worked on?

Over the years, we’ve partnered on numerous high-impact commercial projects—many under NDAs. One of our flagship offerings is SpaRTAN, a multidisciplinary collaboration between:

• Human Developmental Biology Resource – Tissue & slide preparation
• Bioimaging Facility – High-resolution imaging
• Genomics Core Facility – Library preparation & sequencing
• Bioinformatics Support Unit – Advanced data analysis

In 2020, SpaRTAN became the first 10X Genomics Visium certified service provider in Europe, solidifying our position as leaders in spatial transcriptomics.

What does a typical day look like for you?

Our work is really a split between large sample collections (e.g. longitudinal studies, clinical trials) that run over weeks/months, alongside small sample collections, with quick turnarounds. Our services week to week are often a mix of routine RNA-Seq and DNA-Seq workflows alongside more specialist single-cell and spatial transcriptomics projects.

Other activities include working with our customers to provide:

• Troubleshooting – to maximize sample quality and sequencing success
• Consulting – on experimental design, budget planning, and to mitigate against batch effects, and ensure the data yield is appropriate to answer the biological questions being asked
• Project management – e.g. for grant application or during service delivery

We also have high consumables turn-over, so we work closely with suppliers and key account managers, to ensure cost efficiencies.

How do companies engage with you?

Companies engage with us through direct contact or via Newcastle University’s Enterprise Service team, who facilitate:

• Service Level Agreements
• Marketing & Business Development Support
• Customer Relations

We also collaborate extensively with Diagnostic North East (DxNE), fostering partnerships across academia, healthcare, and industry.

Notable collaborations include:

• Bioinformatics Support Unit – Experimental design and data analysis
• Bio Screening Facility – Managing sample handling & quality control
• Flow Cytometry Core Facility – Supporting single-cell genomics
• Newcastle University Protein and Proteome Analysis – Advancing sequencing-based proteomics
• North East Innovation Lab & NovoPath – Co-developing next-gen diagnostic solutions

Examples of Cross facility integrated workflows:

What excites you about the role – and what are the challenges?

What excites me most is the transformative impact of our work. Whether it’s contributing to the Human Cell Atlas or enabling a young researcher’s first genomic study, every project has significance. Our biggest challenges—and opportunities—lie in scaling operations, predicting future technology needs, and staying ahead in a rapidly evolving field.

A key focus is team development—cutting-edge infrastructure is meaningless without skilled scientists to drive innovation.

What is next for the Genomics Core Facility?

Genomics continues to be a rapidly evolving space, and we must be mindful of charting a course that maximises the benefit to our partners and their research and analysis requirements. This is challenging and in turn more exciting than ever, especially in translational research

In 2025, single-cell and spatial transcriptomics have transitioned into mainstream adoption, with a wider array of commercial solutions now available. Moving forwards, our priorities include:

• Expanding our sequencing capabilities to align with emerging technologies
• Educating and empowering partners on multiomic workflows
• Investing in the professional development of our team to future-proof the facility

How can you be contacted?

If you’re interested in working with us, please reach out to discuss tailored solutions for your research and commercial needs.

Tel: +44(0)191 241 8650
E-mail: jonathan.coxhead@newcastle.ac.uk
Website: https://www.ncl.ac.uk/gcf/
LinkedIn: https://www.linkedin.com/showcase/research-facilities/

Jonathan Coxhead, PhD
Biosciences Institute
Newcastle University
Bioscience Building
Central Parkway
Newcastle upon Tyne
NE1 3BZ