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Research Genome Center

Research Genome Center

 Your partner for genomics related services Facility
Your partner for genomics related services
We are an expertise center that support researchers with their next generation sequencing and genotyping projects. We offer, implement and develop state-of-the-art genomics techniques and tools used in medicine and life sciences research.

We aim to stimulate research and innovation by sharing our expertise, usage of available resources, increasing knowledge transfer and subsequently generating stronger interactions and collaborations between research groups.

The UMCG Research Genome Center consists out of three separate core facilities each with their own expertise to help you with every step of your genomic analysis project.
Relevance

How our research benefits to society

Our center comprises the following facilities:

  • The Research Sequencing Facility is a dedicated research infrastructure that provides support for NGS-based projects to UMCG and RUG research groups but also to external clients from academia and industry. For this, we will not only facilitate the expeditious sequencing of NGS libraries either prepared by research groups themselves or by the facility on behalf of the researcher, but also implement the latest NGS techniques used in medicine and life sciences research, and (co)develop and implement new state-of-the-art NGS techniques to keep NGS-dependent research in the UMCG at the forefront. Furthermore, we advise the researchers on the set-up of their NGS experiments and train researchers in the production of NGS libraries if they would prefer to do this themselves.

    We are experts in single-cell DNA sequencing and the only sequencing facility offering the Strand-seq technology as a service. Strand-seq is a powerful tool to identify besides copy number alterations also copy-number neutral structural genomic aberrations such at inversions and translocations, all at the single cell level thereby preserving tissue heterogeneity. Besides Strand-seq we also offer single-cell whole genome sequencing (scWGS), a shallow single-cell sequencing platform to identify copy number alterations, structural and numerical chromosomal abnormalities at single-cell resolution to uncover cellular diversity in heterogeneous samples.

    The Research Sequencing Facility is part of the European Research Institute for the Biology of Ageing (ERIBA) and is a DTL-hotel, a Dutch techcentre for life sciences.

  • The Genome Analysis Facility is part of the section Genome Diagnostics of the Genetics department of the UMCG. All our genome diagnostic tests are offered for your research questions, such as exome sequencing, genome wide SNP arrays, and DNA and RNA isolations.

  • The Genomics Coordination Center is the UMCG expertise hub for ‘omics’ data analysis, integrative bioinformatics and FAIR data stewardship. We provide tools, services and courses for researchers and bioinformaticians to accelerate scientific research and collaborations.

    The Genomic Coordination Center is part of the Genetics department and is a DTL-hotel, a Dutch techcentre for life sciences.

     

Service Request

If you would like to use one of our services, please refer to the relevant service for contact details and fill in Research Genome Center intake form.

Your request will be reviewed by the appropriate team members. We will contact you to discuss further steps.

 

  • Services are subject to a fee, which depends on the type of service requested but usually includes costs for the use of instrumentation (service contract/depreciation), personnel, consumables, and overhead costs (includes a failure fee to allow for technical problems during the service), in a non-profit manner. Please contact us for an estimation of project costs using the intake form.

Services

  • We provide manual and automated nucleic acid isolations (RNA, gDNA) from various samples using a variety of isolation kits from Promega and Qiagen. We will subsequently perform quality control to measure the concentration and integrity of the isolated nucleic acid. We are currently investing in infrastructure to automate nucleic acid isolation in a more high-throughput manner, thereby drastically increasing our capacity to process more samples simultaneously. Please contact us for more information regarding nucleic acids isolation using the intake form.

  • High-quality samples are crucial for successful analysis. It is therefore essential to not only quantify your samples but also to check the integrity and/or fragment size of your RNA, DNA (gDNA/cDNA) and final NGS library. We have a number of quantification options available:

    1. Nanodrop: RNA & DNA quantification based on spectrophotometric analysis
    2. Qubit Fluorometer: RNA & DNA quantification based on fluorometric analysis
    3. TapeStation 4200: High-throughput automated capillary electrophoresis (1-96 samples) for accurate RNA & DNA quantification and integrity analysis. Analysis time is ~ 2 minutes per sample or 90 minutes for 96 samples
    4. Fragment Analyser: Medium-throughput automated capillary electrophoresis (1-96 samples) for accurate RNA & DNA quantification and integrity analysis. Analysis time is ~ 5 minutes per sample or 8 hours for 96 samples

    We can measure the concentration and integrity of your research RNA or DNA samples twice a week (Tuesdays & Thursday). The results of the quality control (QC) analysis are sent via E-mail to the researcher. Alternatively, we can teach you to perform the QC analysis yourself, which requires an obligatory training on our TapeStation and/or Fragment Analyser system. Please contact us for more information regarding QC analysis using the intake form.

  • Profiling of single nucleotide polymorphisms (SNPs) and structural variants is commonly used in genetic research. SNP markers are widely used to study the association of genes with complex disorders, for linkage studies in Mendelian disorders, and to find structural genomic variations.

    We have an automated system for generating genome-wide genotyping data using Illumina Infinium arrays. We offer GSA arrays for small scale project; for large scale projects we may process Illumina arrays of your choice, when this fits our robotic system. Please contact us for more information regarding array analysis using the intake form.

  • Next-generation DNA sequencing allows the comparison of the genetic content among samples and the identification of germline and somatic genetic variants, such as single nucleotide polymorphisms (SNPs), insertions and deletions, and copy number variants (CNVs). We offer the following DNA sequencing applications:

    1. Agilent Exome DNA sequencing: We offer exome sequencing using Agilent SureSelectXT Human All Exon V7 capturing kits.
    2. Agilent Targeted DNA sequencing of selected gene panels: We offer several selected gene panels for research purposes.
    3. Small genome / amplicon / cDNA sequencing: We offer Nextera XT DNA library preparation and subsequent sequencing
    4. Low-input whole genome sequencing (WGS): Shallow whole genome sequencing of low input samples (e.g. 30-50 cells) upon fluorescence-activated cell sorting (FACS) for CNV and aneuploidy detection.

    Library preparation is performed using automated liquid handling robots preconfigured for library preparation in 96-well plate format (e.g. the Agilent Bravo NGS workstation or Magnis system). Upon library preparation and QC analysis, libraries are sequenced in house on an Illumina MiSeq or NextSeq 500 sequencer, or outsourced on a NovaSeq system, depending on the scale of the project. Please contact us for more information using the intake form.

  • RNA sequencing, or transcriptome sequencing, provides not only precise measurement of RNA transcript levels, but it can also be used to discover novel transcripts, alternative splicing, or allele-specific expression. We offer several RNA sequencing applications:

    1. NEXTFlex Rapid Directional qRNA-seq (Perkin Elmer): Full length RNA-seq library preparation that features strand-specific RNA sequencing and correction of PCR amplification bias by molecular indexing: during library preparation molecular barcodes are incorporated which can be used to accurately remove duplicate reads and thereby allows RNA molecule counting (quantitative (q)RNA-seq). This approach can be applied to poly(A)-enriched RNA (analysis of coding transcripts) or ribosomal (r)RNA-depleted RNA (analysis of coding and non-coding transcripts).
    2. Lexogen QuantSeq 3’mRNA-seq (Isogen Life Science BV): Library preparation protocol generating stranded libraries of sequences close to the 3’ end of polyadenylated RNA. QuantSeq uses total RNA as input, so prior poly(A) enrichment or rRNA depletion is not required. Option to incorporate unique molecular identifier sequences during second strand synthesis allows unique tagging of individual transcripts to identify PCR duplicates and eliminate amplification bias.
    3. Smart-3SEQ (in-house protocol): Cost-effective library preparation protocol generating stranded libraries of sequences close to the 3’ end of polyadenylated RNA (Foley et al; PMID 31519740). Smart-3SEQ uses total RNA as input, so prior poly(A) enrichment or rRNA depletion is not required. Standard incorporation of unique molecular identifier sequences during reverse transcription allows unique tagging of individual transcripts to identify PCR duplicates and eliminate amplification bias.
    4. Low-input RNA-seq (New England Biolabs, Takara or in-house protocol): Expression analysis of samples containing low amount of RNA or just a few cells (e.g. 30-50 cells) upon fluorescence-activated cell sorting (FACS).

    Library preparation is performed using the Agilent Bravo NGS workstation, an automated liquid handling robot preconfigured for library preparation in 96-well plate format. Upon library preparation and QC analysis, libraries are sequenced on an Illumina NextSeq 500 sequencer. Please contact us for more information using the intake form.

  • Single cell sequencing allows the analysis of transcriptome (scRNA-seq, immune profiling, CITE-seq, CRISPR screens, spatial transcriptome), epigenome (scATAC-seq), and genome (scWGS, Strand-seq) at single-cell resolution to uncover cellular diversity in heterogeneous samples. We offer the latest technology available on the market:

    1. 10X Genomics® ChromiumTM platform
    2. Takara ICELL8 Single-Cell system
    3. Cellenion CellenONE F1.4 platform
    4. Plate-based single-cell sequencing platform of single cells isolated by fluorescence-activated cell sorting (FACS) using a BD FACSJazzTM Cell sorter available at ERIBA and Agilent Bravo liquid handling robot for library preparation.

    Upon library preparation and QC analysis, libraries are sequenced on an Illumina NextSeq 500 sequencer. Please contact us for more information using the intake form.

  • For researchers preparing their own NGS sequencing libraries (e.g. RNA-seq, ATAC-seq, ChIP-seq, Sure-Seq, and/or single cell omics variants), we offer standalone next generation sequencing as a service using an Illumina NextSeq 500 or MiSeq sequencer.

    1. NextSeq500 High Output runs:
      • output 25 - 120 Gb
      • ~ 400 million clusters
      • Single-end run options for 75 or 150 cycles
      • Paired-end run options for 40, 75, or 150 cycles
    2. NextSeq500 Mid Output runs:
      • output 16 - 39 Gb
      • ~ 130 million clusters
      • Single-end run options for 150 cycles
      • Paired-end run options for 75 or 150 cycles
    3. MiSeq, divers sequencing kits:
      • output 300 Mb - 15 Gb
      • Single-end run options for 36, 75, 150 or 300 cycles
      • Paired-end run options for 75 or 150 or 300 cycles

    We accept individual or pooled libraries for which we can perform the quantity and quality assessment, and pooling in case of individual libraries before sequencing. Alternatively, the researcher can perform these assessments him- or herself but is obliged to provide QC information to determine if the quality of the superpool meets our requirements.

    Apart from our in-house sequencing service, we offer preliminary data analysis including demultiplexing of the raw sequencing data, subsequent alignment to the reference genome of interest and generation of gene count lists using automated bioinformatics pipelines. Furthermore, we can help you with downstream analysis of small-scale omics projects. However, if you need help with more advanced data analysis, we will refer you to the Genomics Coordination Center. Please contact us for more information using the intake form.

  • We can advise and facilitate your large-scale NGS projects and bring you in contact with our collaborating partners. Please contact us for more information using the intake form.

    1. Multi-omics data integration, processing and analysis
    2. Big data storage and high-performance computing (HPC) facilities
    3. Rare disease and variant/patient databasing, data processing and analyses
    4. Allround Biobank and cohort data support, including catalogue, harmonisation, data capture, data integration, data storage, and analysis
    5. FAIR data software (MOLGENIS) FAIR data stewardship support and courses
    6. Big Data access to Genome of the Netherlands (GoNL)

    Please contact the Genomics Coordination Center via the website.

Contact

Research Sequencing Facility

Diana C.J. Spierings, Head of Research Sequencing Facility

University Medical Center Groningen (UMCG)
European Research Institute for the Biology of Ageing (ERIBA)
Research Sequencing Facility
PO Box 196, Internal Zip Code FA50
9700 AD Groningen
The Netherlands

Visiting address
University Medical Center Groningen (UMCG)
European Research Institute for the Biology of Ageing (ERIBA)
Research Sequencing Facility
Antonius Deusinglaan 1, building 3226
9713 AV Groningen

Genome Analysis Facility

Cleo van Diemen, Coordinator Genome Analysis Facility
Martijn Viel, Coordinator Genome Analysis Facility

University Medical Center Groningen (UMCG)
Department of Genetics
Genome Analysis Facility
PO Box 30.001
9700 RB Groningen
The Netherlands

Visiting address
University Medical Center Groningen (UMCG)
Department of Genetics
Genome Analysis Facility
Antonius Deusinglaan 1
9713 AV Groningen

Genomics Coordination Center

visit the GCC