Single-Cell Core

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Genetic alterations play a key role in the initiation of a range of diseases. For instance, in cancer there are tumor clones with distinct genetic alterations, such as single nucleotide variations (SNVs), copy number variations (CNVs) and indels. This heterogeneity is vital to tumor development, proliferation and metastatic potential, while also playing a key role in therapy resistance. Single-cell sequencing is used to investigate the (epi)genome of single cells and to unravel the concept of heterogeneity.

In recent years, many novel sequencing technologies have been developed in the research groups of Alexander van Oudenaarden and Geert Kops. To make these techniques widely available, Single-Cell Core was launched in 2020. Located at the Hubrecht Institute, we have had early access to technologies that no other labs have been running yet. This allowed us to develop a unique expertise on services involving chromatin profiling and karyotyping, giving us a head start in the field of single-cell DNA sequencing. Since then, Single-Cell Core has expanded its client portfolio from research institutes at the Utrecht Science Park, to medical centers in the Netherlands and to science organizations abroad.

Technologies that we currently offer include single-cell chromatin immunocleavage sequencing (scChIC-seq), single-cell transcriptome + chromatin immunocleavage sequencing (scTChIC-seq), single-cell karyotype sequencing (scKaryo-seq) and single-cell EdU-sequencing (scEdU-seq).

Ombion Centre for Animal-free Biomedical Translation

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Ombion Centre for Animal-Free Biomedical Translation is a centre for valorisation and dissemination of animal-free innovations and expertise. We aim to improve and accelerate the translation of new biomedical innovations to patients and users, at lower costs, and without the use of animals. We offer a professional network, courses, and labs for automation, demonstration and education.

Facilities and Services

– Ombion offers unique expertise in model development, assay miniaturisation and standardisation
– Annual summer schools and trainings on automation and the latest advances in in vitro technology
– 600m2 of total lab space for animal-free research of which almost 200m2 dedicated to education
– Over 400m2 of office space, for Ombion personnel and guest researchers
– State-of-the-art cell culture labs and molecular biology labs
– An education and training lab featuring cell culture facilities and automated equipment
– Advanced confocal microscopy, tailored to 3D cell culture models and assays in miniaturised format
– Unique robotic automation to support assay miniaturisation and standardisation of advanced three-dimensional cell culture assays like organoids

Capabilities

– Assay development, miniaturisation and standardisation in ML-I or ML-II conditions
– Regulatory routing
– AI
– Automation and medium-to-high throughput screening in ML-I labs
– High-content screening and image analysis

Users

– Personnel of Ombion, including those of the Transition Projects based at several UMCs and research centres
– The Ombion network
– External professionals in the Netherlands and abroad

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Hubrecht Imaging Center

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Imaging is becoming increasingly important in the biomedical sciences and in research at the Hubrecht Institute. To meet the growing demand for advanced imaging equipment, the Hubrecht Imaging Center (HIC) was established in 2009. In recent years, the Hubrecht Institute has acquired a range of state of the art microscopes, which are now managed by the HIC.

The HIC supports a wide spectrum of imaging needs, from simple phase contrast imaging to high resolution imaging of living tissue. Advanced systems ar available at the HIC include confocal, two photon, TIRF, FRAP, STED and FRET microscopy, including FLIM. We have also spinning disk systems and light sheet microscopes.

The HIC ensures that the Hubrecht Institute’s advanced imaging equipment functions optimally and is used to its full potential. This is achieved through regular system testing and optimization, training new researchers, and providing support for imaging experiments.

Pathology Research Core

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The Pathology Research Core (PRC) facility offers a broad range of tissue collection, processing and analysis techniques to facilitate biomedical and clinical researchers. We collect preclinical and clinical samples and process them for analyses and storage.

Samples are collected as fresh frozen specimen, processed for formalin-fixing and paraffin embedding (FFPE), or prepared for electron microscopy (EM).

We have a vast range of antibody-based protein expression detection techniques (chromogenic and fluorescent) and chemical procedures for histopathological assessment.

Our facility can also culture and process/analyze patient derived tumor organoid PDO models in specified extracellular matrix (ECM) gels upon request.

We provide high-quality histopathological services to support research into human and non-human (mouse, rat, fish) healthy and diseased tissues

Westerdijk Fungal Biodiversity Institute: Culture collections and databases

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The Collection and databases facility of WI-KNAW maintains two important collections of microbes: the world-renowned CBS Collection for filamentous fungi and yeasts, founded in 1904 and one of the oldest and largest culture collections for fungi in the world; and the NCCB collection, a historically important collection of wild-type and mutant bacterial strains and phages.

Its holdings cover a broad range of the culturable fungal diversity, with strains originating from various habitats on all continents and in the seas, and over 16 000 type strains that serve as important references for taxonomy. Yearly, 4 000 – 6 000 strains are supplied to requestors in around 50 countries for research and development, and 2 000 – 3 000 new strains are deposited from various origin and substrates. All strains are DNA sequenced for quality control and identification purposes, the fungi mostly by ITS and LSU rDNA, and bacteria by (partial) 16S. New data including on physiology, mass spectrometry (MALDI-TOF) and other data are continuously generated and linked to the strains. For many strains whole genome sequences are also available.

  • 100 000 strains of filamentous fungi and yeasts in CBS
  • 10 000 strains of bacteria and actinobacteria, and 560 phages in NCCB
  • Strains are preserved in a metabolically inactive state, by lyophilization (freeze-drying) and cryopreservation. A smaller part is also actively kept on agar media.
  • Online databases providing open (meta)data to search strains and to perform analyses
  • Supply of cultures in active state on agar media, as freeze-dried ampoules or genomic DNA extracts
  • Deposit of novel living strains in the public collections (free-of-charge, acceptance pending quality and compliance checks)
  • International Depository under the Budapest Treaty (patent strains, fee charged)
  • Safe deposit service (fee charged periodically)
  • Quality assurance according to ISO 9001

UMC Utrecht Biobank Research Ethics Committee (TCBio)

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TCBio reviews procedures that collect and/or use human biological materials for medical scientific research to ensure high quality biomedical research and responsible collection, storage, management and distribution of human tissue, cells and related data. The committee is composed of experts in clinical practice, biomedical research, genetics, methodology, ethics, law and participant experience ensuring compliance with Dutch and European regulations.

For a more information see: https://tcbio.umcutrecht.nl/en/

Ethics review, METC and non-WMO biobank research

Researchers looking for METC or MREC guidance for biobank research at UMC Utrecht may also need to consult the Biobank Research Ethics Committee (TCBio). TCBio reviews the collection, storage, management and research use of human biological material and related data when the research is not subject to the Dutch Medical Research Involving Human Subjects Act (WMO).

For WMO-regulated research, review by an accredited Medical Research Ethics Committee (METC/MREC) or the Central Committee on Research Involving Human Subjects (CCMO) may be required. When human biological material is used as part of a WMO research protocol already approved by a METC, additional TCBio approval is generally not required.

Medical research ethics committee (MREC) NedMec

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Medical Research Ethics Committee (MREC/METC) NedMec

MREC NedMec, also known in Dutch as a Medisch-Ethische Toetsingscommissie (METC), is accredited by the Central Committee on Research Involving Human Subjects (CCMO) to review medical scientific research with human subjects.

MREC/METC NedMec reviews research that is subject to the Dutch Medical Research Involving Human Subjects Act (WMO), the EU Clinical Trial Regulation (CTR), the EU Medical Device Regulation (MDR), and the EU In Vitro Diagnostics Regulation (IVDR).

Through its national scope, MREC/METC NedMec reviews research proposals for researchers, health care organisations, government institutions and other organisations in the health care sector.

Princess Máxima Center Big Data Core Facility

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The BDC provides support and services in the following areas:

Genomics data analyses: development and maintenance of bioinformatics pipelines for bulk sequencing (WGS, WES, RNA-seq) in tumor and organoid samples, processing of nanopore sequencing samples, and development of custom data analyses for research.

Cloud engineering: development and deployment of end-to-end cloud solutions for bulk sequencing data—integrating a cloud-native data warehouse, portals (e.g. NL-4C), and secure APIs with a centralized governance to accelerate the delivery of genomic insights to researchers, clinicians and benefit patient care.

Dutch Comprehensive Childhood Cancer Commons: or NL-4C is a cloud-based portal developed by the BDC that enables data visualization, exploration and building of virtual datasets of harmonized genomic and clinical data of the children with cancer treated at the Princess Máxima Center.

Data stewardship: coordinating and promoting appropriate data management and stewardship practices for preclinical data, including implementation of the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles, to ensure optimal data (re)use.

Innovation Lab (iLab)

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Located in the Utrecht Science Park, iLab provides easy access to University of Applied Science Utrecht (UASU, Hogeschool Utrecht (HU) , Lectoraat Innovative Testing in Life Sciences & Chemistry, Institute for Life Sciences & Chemistry (ILC).

At iLab, ideas do not stay on paper – they get built, tested, and proven.

Startups, SMEs, corporates, and public organizations are invited to use iLab as their innovation playground: a place to prototype, experiment, and validate new concepts quickly and safely. With an ISO-certified lab infrastructure and a wide range of advanced equipment, iLab helps reduce development risks and accelerates time to insight.
What truly sets iLab apart is its unique position at the intersection of education, research, and industry. iLab connects external partners directly with the applied expertise of UASU-HU, enabling real-world experimentation, hands-on learning, and meaningful knowledge exchange. Whether you are exploring an early-stage technology, testing a bold new idea, or refining a concept for market readiness, iLab offers the environment to move forward with confidence.
By working at iLab, you gain access not only to state-of-the-art facilities, but also to multidisciplinary teams of researchers and motivated students who bring fresh perspectives and practical skills. Together, we turn challenges into opportunities and innovation into real societal impact.

If you’re ready to experiment, collaborate, and build what’s next – iLab is open to you.

Single Cell Discoveries

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We are the transcriptomics experts

We have worked with single-cell since the early days, across multiple technology generations. Across 50+ organisms and 30+ tissue types, we’ve seen how workflows behave in real biological edge cases. That experience helps us anticipate risks early and deliver decision-ready data.
We continuously evaluate new platforms through internal R&D and real-world validation. We adopt technologies only when they clearly improve data quality, robustness, or interpretability. When commercial options fall short, we build and validate proprietary assays and workflows.
We act as a thought partner, not just a service provider. We help shape experimental design, make trade-offs explicit, and align work with downstream objectives. This approach supports complex, multi-phase programs where confidence and consistency matter.

Our services include:

  • Single Cell workflows:
    • SORT-seq
    • VASA-seq
    • 10x Genomics: all solutions
    • Parse Biosciences solutions
  • Bulk RNA-seq:
    • mRNA bulk RNA-seq
    • Total bulk RNA-seq
    • Discovery-seq: high throughput bulk RNA-seq
  • Multiomics:
    • 10x Genomics Multiome
    • BioSkryb Genomics’ ResolveServices™
    • High-throughput FFPE Proteomics
    • Olink proteomics

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