Biocenter Oulu Sequencing Center

Information about the service:

For sequencing of multiple targets at the same time, we offer next –generation sequencing using two different platforms: Illumina’s NextSeq550 and Oxford Nanopore Minion.

More information about the service.

Information about the service:

Capillary sequencing is offered with ABI3500xL Genetic Analyzer-system.

More information about the service.

Information about the service:

• Isolation is done with QIAsymphony SP instrument
• The purity and concentration of isolated DNA is determined spectrophotometrically
• For further information, please contact: Annika Väntänen, tel. +358-(0)294 48 5752 or annika.vantanen (at) oulu.fi, lbkseq (at) oulu.fi

Information about the service:

• Automated pipetting can be done with QIAgility, which is a compact benchtop instrument offering rapid and reliable pipetting
• Examples of applications: Real-time RT-PCR setup, normalization, serial dilution, restriction digestion and PCR setup. Explore the virtual demo to learn more
• Reservations using the Asimov system. New users! Before the first reservation contact the core facility for training.
• Located in Aapistie 5, Rm 276B
• Price: 3.0 € per hour (~ plate). Customer provides the plastics.
• Contact: lbkseq (at) oulu.fi

Information about the service:

• Automated electrophoresis (sizing, quantitation and quality control) is done with Agilent 2100 Bioanalyzer system
• Customer delivers diluted aliquots of DNA/RNA samples
• Eleven/twelve samples can be processed with one chip
• Contact: ngs (at) oulu.fi

Pricing info

Prices are indicated as VAT 0%

Service request form

Bioanalyzer form

Details and specifications for Agilent 2100 bioanalyzer assays

Samples have to be delivered in a suitable buffer and concentration.

Following kits are available:

Agilent High Sensitivity DNA Kit

Separation, sizing and quantification of low concentrated dsDNA samples from 50 to 7000 bp.

%CV= coefficient of variance

Agilent DNA 1000 Kit

For the separation, sizing and quantification of dsDNA fragments from 25 to 1000 bp.

%CV= coefficient of variance

Agilent RNA 6000 Nano Kit

For the analysis and quantitation of total and mRNA samples of 25 to 500 ng/µL in concentration.

%CV= coefficient of variance

Information about the service:

• BioRad (CFX96 Touch™ Real-Time PCR Detection System) is offered for use as self-service
• Reservations can be made through iLab
• Located in Aapistie 5, Rm 444B
• Usage price 1.2 € per hour
• Contact: lbkseq (at) oulu.fi

If unfamiliar with the Biorad CFX96 Touch™ Real-Time PCR Detection System, ask for introduction from the core personnel.

Plates:

• Use only low-profile plates! Using other plates will harm the lid system.
• To avoid evaporation of samples it is recommended to use skirted plates
• Plates recommended (Bio-Rad) low-profile, skirted: HSP-9601, HSP-9655, HSP9631, HSP9901, HSP9955, HSP9611, HSP9621, HSP9635, HSP9641, HSP9645, HSP9661, HSP9665, HSP9666, HSP9601B

If there are any problems or you get error messages, record them in the booklet and inform the personnel.

Services

Optical genome mapping

General information

Optical Genome Mapping (OGM) is a technique that provides a comprehensive view of the structural variants in the genome. It can be applied in various contexts, such as genomic profiling of cancer, quality control of cell lines (genomic integrity), and detection of disease-causing structural variants in human diseases.

Instrument

Bionano Saphyr optical genome mapping system

Sample requirements

For the isolation of ultra-high molecular weight DNA, a variety of fresh or fresh frozen sample types can be used, including blood, cultured cells, tissues, tumor biopsies, and bone marrow aspirates.

Contact information

tuomo.mantere@oulu.fi, ngs@oulu.fi

Useful link

https://bionano.com/how-ogm-works/