Research Genome Center

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® Chromium^TM 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 FACSJazz^TM 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.