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 a discussion of experimental design with Dr. Lisa White, director of the MCF. She will meet with you 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 sigficance? (See how increasing replicates can dramatically affect your data.)
- How do you intend to analyze and interpret your array results (a lab technician, a statistician, yourself, the MCF)?
Researchers should also review the MIAME standards on the MGED (Microarray Gene Expression Data Society) website. MIAME (Minimum Information About a Microarray Experiment) is the new standard for submitting microarray data for publication.
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 preparers
- 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 MCF 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 assurred that the majority of detected variation is biological.
A good starting reference for any researcher thinking about using microarray technology is a recent paper in Nature Reviews Genetics: Expression Profiling - Best Practices for Data Generation and Interpretation in Clinical Trials. It gives a good introduction into the best practices for performing a microarray study.
Another great reference is on the Nature website. They recently added a new review section on microarrays. There are several articles on recent developments and discoveries using microarray technology. In particular please look at the article on the different ways to analyze microarrays and the issues and problems that can occur when interpreting those results. Please feel free to view the article: The Use and Analysis of Microarray Data
To learn more about how to design your next microarray experiment, please contact the Microarray Core director, Lisa White, to set up an appointment.