A. We currently utilize spotted DNA glass arrays . In the generic arrays, libraries of oligonucleotides (50 or 70mers) are printed onto coated glass. The custom made arrays could be either oligonucleotide libraries or purified PCR products. We perform indirect amino-allyl labeling of the sample and reference RNA and couple the cDNA produced with Cy3 and Cy5 dyes. The slide is then hybridized with the Cy3 labeled sample plus a Cy5 labeled reference cDNA. We strongly recommend a “dye swap” scheme where a replicate slide is hybridized with a Cy5 labeled sample plus a Cy3 labeled reference cDNA. Following washes to remove unbound and non-specific hybridization, the slide is scanned using a laser confocal scanner that excite the respective dyes and generate signals in two different channels. The fluorescence intensities are then quantified and the data is processed trough a series of steps that include slide QC, Normalization, Technical and Biological analysis and Classification methods.

Q. How do I design an experiment using microarray technology?

A. An appropriate experimental design is key when using this technology. Some of the issues you have to consider when planning an experiment include: questions you are trying to answer and how many biological and technical replicates are needed to obtain statistical significance. Technical factors like quality and quantity of RNA that can be obtained from specific samples or the quality of PCR products to be spotted on a custom made array, are also extremely important for the outcome of the experiment. Our laboratory has many years of experience in the design of microarray experiments. We are researchers too and therefore understand the importance of a well-planed experiment. When you contact us regarding a microarray experiment our expert team will gladly advice you on the complete design of the experiment

Q. What are the guidelines for RNA preparation and submission?

A. The outcome of a microarray experiment depends greatly on the quality of the starting RNA. RNA should be extracted using a method that produces high quality RNA. We recommend the use of TRIZOL reagent (Invitrogen) and/or column purification system like RNAsy (Qiagen). RNAs must be Dnasa treated. The labeling protocol requires 75ug of Total RNA per dye. In a dye swap scheme each sample requires two labeling reaction (Cy3 and Cy5), therefore 150ug of Total RNA are required per sample. For samples in which only limited amount of RNA can be obtained, we perform a labeling protocol that involves linear amplification and the stating RNA material can be as little as 0,8ug of total RNA. RNA pellets should be sent in microcentrifuge tubes with 70% ethanol in dry ice by courier or brought in person. Quantity (absorbance at 260, 280 and 320 nm) and Quality (gel picture showing rRNA bands) data should be included along with the samples. We will gladly provide you with protocols to be used as guidelines for RNA extraction and quality assessment of your RNA.

Q. What are the guidelines for submitting PCR products for custom printing?

A. The starting point in a microarray experiment is the array itself. As such it is extremely important to produce arrays of high quality. In our laboratory, we have optimized factors like slide type, spotting buffer and spotting pins in order to produce high quality arrays. However the quality of the array will greatly depend on the quality of the DNA material to be spotted. There should be a unique PCR product per clone amplified at a concentration of at least 200ng/ul. 100ul of each PCR product should be send in a 96 well format plate (preferably) in dry ice or brought in person.

Q. What are the prices for the services?

A. If you are interested in any of our services described above, contact us and we will provide you with a quote for your evaluation.

Q. What is the turn around time?

A. Once you contact us and have an initial meeting to discuss the experimental design, we will give you an estimate of the time to complete the experiment that depends on the magnitude of the project.

Any more questions? Contact us at:

Gentron Genomic Services
Gentron Inc. Suc. Argentina
Roque Sáenz Peña 778
San Isidro (1642)
Buenos Aires, Argentina

Phone: 00 54 114 747 4848
Fax:       00 54 114 747 4848