DNA sequencing is a reading process of the nucleotide bases found in a DNA molecule. For more than 25 years sequencers have helped in many scientific progresses such as the first compete human genome sequencing and the discovery of many genes linked to different diseases.

Sanger sequencing through capillary electrophoresis is the highest quality standard in DNA sequencing and is used in a big amount of scientific laboratory experiments.

Offered services:

• Simple sequencing. Fragments of 100-500 pb.
• Long sequencing. To be authorized by the person in charge. Fragments of 1100-1300 pb.
• Fragment analysis.
• Device-compatible commercial kits.

These services include a sequencing run on the ABI Prism 3130, quality control and delivery of results, PCR product purification (optional) and sequencing reaction plus purification (optional).

Sequencing services rates of the Biogipuzkoa HRI Genomics Platform

Sanger sequencing sample requirements

Technical specifications:

Sequencer ABI Prism 3130 (Life Technologies): 16-capillary.

Genetic information digitization (DNA) and the use of a massive array of parallel sensors allows for a quick and accurate sequencing. Applications for this new technology include: complete sequencing of reduced and viral genomes, mitochondrial sequencing, sequencing and quantification of microRNAs and tailor-made kit sequencing with genes of interest.

Technical specifications:

• PGM.
• OneTouche 2 and OneTouche ES.
• 50 Hz sonicator.
• Thermal cycler (Life Technologies).
• Qubit spectrophotometer.
• E-Gel base electrophoresis box.

The Biogipuzkoa HRI Genomics Platform is a benchmark agent in Ion Torrent technology use.

DNA Microarray technology allows researchers to analyze a big deal of gene expressions over a unique reaction in fast and efficient manner.

Thousands of probes (with known identity) get immobilized into a solid bracket. A typical microarrays experiment includes the mRNA hybridization (of its cDNA) into its DNA homologue in the array. The mRN quantity linked to each place in the array indicates the expression level of the different genes.

Offered services:

The use of the platform array technology is on offer for any of the possible applications.

The service may involve either using the machine, in this case the user must prove his ability to use the entire platform and it will be his responsibility to obtain all the consumables and other materials necessary for the experiments; or the full service, in which the user only needs to deliver the samples and the necessary information for the project.

Microarrays services rates of the Biogipuzkoa HRI Genomics Platform

Technical specifications

• Platform GeneChip Affymetrix
• Hybridisation oven: GeneChip Hybridization Oven 640
• Washes and staining: GeneChip Fluidics Station 450
• Reading: GeneChip Scanner 3000

Results from experiments with microarrays generally need to be validated with other platforms, and the real-time PCR platform is the most commonly used. The Genomics Platform is therefore a comprehensive solution covering all steps from processing the microarray to validating the results through different technologies such as real-time PCR.

Real-time PCR or quantitative PCR is a variation of the standard PCR and it is used for quantification of DNA or messenger RNA (mRNA) in a sample. By using primers specific to a sequence, it is possible to determine the number of copies or the relative amount in a given DNA or RNA sequence.

Offered services:

The use of the platform quantitative PCR technology is on offer for any of the possible applications. The service may involve either using the machine, the user who is familiar with the technique smears a plate prepared by him; or include technical assistance and technology design.

Methodological support includes advice on designing the experiments and asking the person in charge any questions that may arise in the course of the project. The user can use the consumables and other materials available on the platform; as for the plates, he can use his own or the ones available on the platform.

Real-time PCR services rates of the Biogipuzkoa HRI Genomics Platform

Technical specifications:

• System “LightCycler 96 (LC96) (Roche): 96-well block”.
• System “CFX96 Touch (BioRad): 96-well block”.
• System “CFX384 Touch (BioRad): 384-well block”.

Real-time PCR primer and probe design

ddPCR (Droplet Digital polymerase chain reaction) was developed to obtain a precise and absolute quantification of target sequences which is extensively employed in clinic research and diagnosis.

The ddPCR QX200 (BioRad) system combines the water-oil emulsion droplet technology along with microfluidics. The droplet generator divides samples into 20.000 droplets or partitions to amplify each sample through PCR on each droplet. The measurement of positive and negative fluorescent droplets determines DNA concentration.

ddPCR offers  the benefits of absolute quantification together with a high sensitivity. Due to this point, different services are on the rise such as absolute quantifications with no calibration curve, genomic alterations like copy number variations (CNV), rare sequences, gene expression and microRNA analysis, NGS massive sequencing (library quantification, result validation) and single cell analysis.

Offered services:

Access to fungible and any needed material is on offer plus the choice of plate preparation. The user can get and use all the material by himself too.

Digital PCR services rates of the Biogipuzkoa HRI Genomics Platform

Technical specifications:

• QX200 reader.
• C1000 Touch thermal cycler.
• QX200 droplet generator.
• PX1 PCR plate sealer.

The platform offers a large range of tools for precise nucleic acids detection and quantification, such as DNA and RNA, that any researcher may require.

Offered services:

The uses of the bioanalyzer, the spectrophotometer or the fluorometer are on offer, provided that the user has accredited his qualification to use them; or the full service instead.

Please contact the person in charge of the service to check the machine and test availability.

DNA – RNA quality and quantification services rates of the Biogipuzkoa HRI Genomics Platform

Technical specifications:

• 2100 Bioanalyzer (Agilent).

Microfluidics based platform which allows 11 to 12 electrophoresis analysis of RNA, DNA or protein samples in only 30 minutes.

RNA chip combination and its software allow total RNA and messenger RNA (UNAM) quantity and integrity trustworthy determination using minimum sample quantity. Thanks to the quickness, sensibility and result precision of the bioanalyzer it has turned into an essential requirement for RNA sample quality determination previous to microarray genic expression experiment due to its credibility against agarose and polyacrylamide gels. The machine is also useful in NGS library quantification and visualization.

• ND-1000 Spectrophotometer (Nanodrop).

Measures 1µl samples with high precision and reproducibility in order to size purified proteins such as DNA and RNA up while revealing the possible presence of contaminants. Even more the machine can seize highly concentrated samples without diluting them.

• Qubit fluorometer (Invitrogen).

Analytical instrument for DNA, RNA and protein quantification with a higher sensibility and precision than UV absorbance. This fluorometer works with Qubit test kits.

The Qubit fluorometer can be used along with the Nanodrop spectrophotometer to determine DNA or RNA concentration. The fluorometer allows precise quantification of target molecule and the spectrophotometer shows if there is any contaminant.

This high definition scanner produces digital images from fluorescent, chemiluminescent or radioactive samples. The machine is aimed, along with other uses, to bidimensional (DIGE) gel scan.

The use of the scanner is on offer, in this case the user must prove his ability to use the machine; or the full service.

Technical specifications:

• Typhoon TRIO, Variable Mode Imager (GEHealthcare).

Link to Manual and specifications

MAGPIX is a versatile platform with the capacity to carry out multiple qualitative and quantitative analyses of proteins and nucleic acids on a variety of samples. The possibility of carrying out up to 50 determinations in a single reaction volume reduces to the minimum the start quantity, reactive agents and workforce turning this choice into an improved choice of ELISA tests.

The MAGPIX system works using Luminex technology whose magnetic microspheres allow specific analytes to be captured and detected in a sample.

In addition to being able to try out own tests, the market offers a wide battery of tests developed by Luminex partners:

EMD Millipore Corporation

Life Technologies

Bio-Rad Laboratories, Inc.

Offered services:

MAGPIX multiple-reader services rates of the Biogipuzkoa HRI Genomics Platform

Technical specifications:

• Merck Millipore.
• xMAP technology.
• 96 plate reader.

It is estimated that 18% to 36% from all the cell lines used in research are cross contaminated. Due to that issue, currently a big number of publications are wrong or inaccurate and day by day more scientific magazines require the researchers to authenticate their cell lines to publish their articles. (Contact the Cell Culture platform to know more about this service).

Human Cell-line Authentication Service

Human cell-line authentication services rates of the Biogipuzkoa HRI Genomics Platform

The Promote GenePrint 10 System can identify and authenticate human cell lines and detect intra-species contamination. This system is based on specific loci STRs (microsatellite) analysis with the Human Genome which simultaneously amplifies and gets fluorescentely marked by diverse fluorocromes.  The profiles obtained are compared with the ones published for that cell line in ATCC and DSMZ databases.

The user must bring with him a pellet with about 0.5 to 1 million cells.  

The platform of the Biogipuzkoa HRI offers the complete mouse genotyping service. We take charge of putting chips in the mouse pups, DNA extraction, PCR amplification and agarose gel analysis. The obtained results are sent to the users through email.

Offered services:

Users must provide to the service personnel the information related to the sequence of the traces to be used, the PCR conditions and the size of the expected fragments.

The official rates differentiate whether or not put chips in the mouse pups and even to run one or two PCR essays.

In any case, users will bring the reagents and traces for the PCR runs with them and will also pay for the costs linked to the services provided by Animal Facility and Experimental Operations and the agarose gels.

Mouse genotyping rates of the Biogipuzkoa HRI Genomics Platform

Technical specifications:

This process does not require any specific equipment rather than the basic laboratory items.

Moreover, the Computational Biology Platform of the Biogipuzkoa HRI creates synergies and enlarges the efforts made by the Genomic and Molecular Diagnosis Platforms when analyzing large-scale biological datasets that include data quality assessment, comprehensive analysis, results interpretation, communication and presentation in meaningful formats.

Contact the platform responsible to learn more about the characteristics and conditions of its services on offer.