Genomic services

The main area of expertise of the genomics facilities, that are part of the X-omics research infrastructure, consists of guidance and execution of sequencing based research experiments. The services offered by the facilities are described in more detail below.

Consultancy

  • Experimental design
  • Technical assistance

DNA/RNA isolation (from various sources):

  • DNA isolation
  • RNA isolation

Sample prep

  • DNA library prep Illumina: WES (Twist), WGS (PCR free), PacBio: LR-WGS
  • RNA library prep Illumina: TruSeq prep, Illumina prep

Sequencing services

  • Sanger sequencing Thermo Fisher: ABI3730XL
  • Short read sequencing Illumina: Miniseq, Nextseq & Novaseq
  • Long read sequencing
    - SMRT HiFi sequencing PacBio: Sequel IIe
    - Nanopore sequencing Oxford Nanopore Technologies: Flongle, MinIon, GridIon & Promethion

Other services

  • Optical Genome Mapping Bionano: Saphyr
  • Digital spatial profiling Nanostring: GeoMX
  • Spatial molecular imaging NanoString: CosMx
  • SNP fingerprinting Thermo Fisher: Quantstudio 12k Flex Real-Time PCR system

Data processing

  • Mapping
  • Variant calling
  • Differential expression
  • Basic spatial omics analyses Nanostring: GeoMX & CosMX

All services mentioned above are custom services.
Please contact our helpdesk for a quote with turnaround times and prices based on your research question.

Service Description Turnaround time Costs Equipment Data Analysis
Consultancy Advice on the proposed experiment to shape the study design so it yields results compatible with the primary (biological) question 1 - 2 weeks Free    
DNA isolation Isolation of DNA from various tissues/cells/species 1 - 2 weeks €17 - €25 per sample* Hamilton robotics - bead based Not applicable
QiaSymphony (Qiagen)
RNA isolation Isolation of RNA from various tissues/cells/species 1 - 2 weeks €18 per sample* QiaSymphony (Qiagen) Not applicable
DNA library prep Preparation of DNA libraries for short and long read sequencing 1 - 2 weeks €83 Truseq DNA nano* Illumina kits Not applicable
BioMek Liquid Handler
RNA library prep Preparation of RNA libraries for short and long read sequencing 1 - 2 weeks €92 Trueseq RNA polyA* BioMek Liquid Handler Not applicable
€150 Trueseq RNA RiboZero* Illumina kits
Short read/long read sequencing WES, WGS, smMIP target enrichment or amplicon based, from small to large scale 2 - 4 weeks Depending on run type and sequencing set up Miniseq (Illumina) Basic analysis
NextSeq 500 (Illumina)
NextSeq 2000 (Illumina, 2020)
Novaseq 6000 (Illumina)
iSeq-100 (Illumina)
miSeq (Illumina)
Sequel I (PacBio)
Sequel ll (PacBio)
Sanger sequencing Amplicon based 1 - 2 weeks €7 per sample, forward and reverse abi3730XL Basic analysis
Nanopore sequencing Sequencing of single, long molecules (1-100kb+) with Oxford Nanopore technology 1 - 3 weeks € 60 per sample library prep* Oxford Nanopore Flongle Custom pipelines based on community standard, open-source software (like Guppy, minimap2)
€843 Minion run* Oxford Nanopore MinIon
€2343 Promethion run* Oxford Nanopore GridIon X5
Oxford Nanopore Promethion
Saphyr Whole Genome Imaging Optical mapping Custom Depending on run set up Saphyr (Bionano) Data analysis included
SNP fingerprinting Generation of panel based SNP genotypes from low amounts of input material for sample tracing, identification and matching or sampleswap detection  1 - 2 weeks Our standard 60plex SNP panel costs €850 / 45 samples Quantstudio 12k Flex Real-Time PCR system (ThermoFisher) Not applicable
Nanostring (2020) Rapid determination of targeted RNA, DNA or protein levels with the option to link results to microscopically determined regions of interest (digital spacial profiling) Custom custom Nanostring nCounter Max GEO-MX (2020)  
Basic data processing Basic NGS data processing: mapping, variant calling, readcount analyses etc. 1 - 2 weeks €5 / €10 per sample*   Custom pipelines based on community standard, open-source software (like GATK, BWA)
Costs
* Price level 2020 ex VAT and subject to changes.
 

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NWO logoThis research was (partially) funded by NWO, project 184.034.019