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How To Choose The Right Gene Expression Chip

In a previous article, I discussed how to extract high-quality RNA for use in microarray experiments.  Today we’ll talk about how to choose the right gene expression chip for your analysis.  There are many choices out there!  In some cases, you might find that this decision is made for you, as many gene expression chip providers will only focus on certain organisms.

The most common platform is provided by Affymetrix.  This is probably the best place to start looking for a gene chip for your organism of interest.  If you go to their website and enter the common name of your organism into their search box then you can see if they provide a gene expression chip that will be of use to you.

If this is not successful, then you could always look at publicly available gene expression databases such as GEO or ArrayExpress to see what platforms other studies have used for the same organism.

A couple of things to take into account when looking at chips from different companies are:

  • Price – This type of experiment can be very pricey, so make sure you try to find yourself a good deal.
  • Service – Often companies that provide the gene expression chips will not perform in house analysis.  You should have a rep from each company assigned to your area who you will more than likely put you in touch with an institution who already has the required equipment to perform your experiments for you.
  • Analysis – Different levels of analysis will be provided by the various institutions that will run your data.  Some will provide a basic level of analysis for free, others will charge.  Some will do all the analysis at an extra charge and some won’t provide this service at all.  It all depends on how confident you are with statistics as to which option you choose here.  If you have the money to spend then it’s probably best to get somebody to analyse your data for you rather than trying yourself, as I can assure you it won’t be an easy task!

If there is not a company that provides a gene expression chip for you, then there is always the option of designing one yourself.  This may take a lot of time and careful research in order to isolate specific target sequences to hybridize to a glass slide to make your custom made chip, and may not be able to provide as global an output as the readymade versions.  This option is probably best left to the experts – unless there’s really no other way to run your experiment.

How do you choose what microarray chip to use in your experiments?

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