Choosing a Microarray Platform
The choice of microarray platform depends on a number of factors and does not really have a "right" answer. Below are some guidelines to help investigators make their decision.
- Study Organism: Mouse, Human, Rat, Yeast, and Drosphilia are available on both spotted and Affymetrix array platforms. With other organisms, we could design a custom spotted array or you can check out the Affymetrix web site, www.affymetrix.com to view other types of organisms available on arrays.
- Genes of Interest: Most of the arrays available are designated "whole genome", and so there is considerable overlap in the genes queried. There are differences between the platforms, however, and we strongly recommend that investigators check that the platform they are considering carries their gene(s) of interest. We provide lists of the genes within the spotted arrays on our web site, and Affymetrix gene lists can be found at ww.affymetrix.com
To view genes present on various platforms, Chip Comparer, can be used to see the overlap between spotted and Affymetrix array platform.
- Cost: Please view the files posted on our web site for array and processing costs:
Spotted array processing:
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Affymetrix array processing:
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- Two-color Arrays: When using a two-color microarray platform (spotted), we strongly suggest using a common reference design. When using Human, Mouse, or Rat arrays, we recommend using our supplied "Stratagene Universal Reference", this will be labeled with Cy3 for each array. The sample of interest will then be labeled with Cy5 dye. This gives you a "common reference&q on each array so you can compare one sample to another from one array to another. This is the most commonly used design and makes analysis less complicated. If a common reference is not commercially available then the researcher can design one for the experiment. Keep in mind, you will need enough RNA for all samples submitted, i.e. label the wildtype in the Cy3 channel and all other samples in the Cy5 channel.
Another labeling approach is to do a dye swap, i.e. label sample 1 with Cy3 and sample 2 with Cy5, then for another array label sample 2 with Cy3 and sample 1 with Cy5. However, this requires twice as much sample and the data analysis can be complicated.
When requesting microRNA arrays, we suggest using the miRNA reference panel (synthetic microRNA oligos provided by Ambion) as a common reference. We will provide this for a small additional fee. Alternatively, Ambion also has an assortment of FirstChoice Total RNA for mouse and human in most tissue types, which you may purchase for use as a common reference.
- Sample Abundance: While we offer RNA amplification for both spotted and Affymetrix microarray platforms, we recommend that amplification be avoided if at all possible. If amplification is necessary, all samples will need to be amplified. Amplified and unamplified microarray data cannot be compared.
- Collaboration: If you will be comparing your data with someone else's microarray data, you should consider the array platform that was used previously.
- Prior Experience: Some labs have used a particular technology in the past and are comfortable with it. While this should never be the entire basis of your decision, it is something to consider when all else is equal.