Experimental Design

When you first begin to consider using microarray technology to answer questions related to your research, the very first step you should take is discuss your experimental design. The MAD will be happy to talk about your questions and to help construct an effective design that will help you answer those questions using the microarray facilities. There are many factors that must be considered when using microarrays, including:

• What questions are you trying to answer?
• What type of tissue/cells do you plan to use?
• How easy or difficult it is to obtain quality RNA from your samples?
• What RNA isolation technique is appropriate for your chosen tissues or cells?
• How much RNA can you actually obtain from your sample?
• How many replicates are needed to obtain statistical significance?
• How do you intend to analyse and interpret your array results (a lab technician, a statistician, yourself, the MCF)?

There are dozens of experimental variables that may affect microarray experiments, and every researcher's goal should be to eliminate as many of those sources of variation as possible through good experimental design. Some variables to be aware of are:

• Procedural variation - sample collection and RNA isolation
• Technician variation - Arrays are notoriously finicky. Ensuring that the same technician handles all samples in an experiment is necessary.
• Equipment variation
• Reagent variation - different lot numbers and different experimentators
• Starting material - RNA concentration and quality needs to be checked every time; make sure the amount of starting material is the same for every chip in the experiment.

The MAD can reduce many of those variables by providing full service to researchers. We will begin with quality RNA or DNA (provided by the user) and perform all of the sample preparation and chip processing on our equipment. Therefore, the researcher can be assured that the majority of detected variation is biological.

To learn more about how to design your next microarray experiment, please contact the MAD, to set up an appointment.