DNA Microarray Core Facility

Experimental Design

Experimental Design

Microarray results are directly influenced by the experimental design, therefore it is crucial that the researcher control for as many experimental factors within their subjects as possible. The Duke Microarray Facility provides free experimental design consultation to researchers who plan to use our microarray resources. Please contact us at microarray@duke.edu to set up an appointment before starting your experiment or collecting RNA.

Several key guidelines for designing your experiment are highlighted below (referenced from Vanderbilt Functional Genomics Shared Resource ).  Another good starting reference for any researcher thinking about using microarray technology is a paper in Nature Reviews Genetics 2004 March; 5(3):229-37.“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.

General questions to consider when designing your microarray experiment:

  1. What experimental questions are you trying to answer?
  2. What microarray platform do you intend to use?
  3. What type of tissue/cells do you plan to use?
  4. What variation exists between samples, and can it be controlled?
  5. How easy or difficult it is to obtain quality RNA from your samples?
  6. What RNA isolation technique is appropriate for your chosen tissues or cells?
  7. How much RNA can you actually obtain from your sample? Do you need to pool samples?
  8. How many replicates are needed to obtain statistical significance?
  9. How do you intend to analyze and interpret your array results?

Patient Samples. When submitting patient samples, please keep the following in mind:

  1. We are not a HIPAA-compliant facility. All human samples must be completely de-identified before we see them - the tubes should only have the deidentified labels on them, do not include any identifying information on the sample submission sheet.
  2. We are not a clinical laboratory. All of our procedures are approved for research only, not for diagnostic purposes.
  3. Humans have a very deep genetic pool - much deeper than any laboratory animals. For example, there will be, on average, more variations in human samples than mouse samples, and the variables are harder to control. For instance, human replicate samples are rarely "litter mates". Therefore, when possible, for human studies we advise the use of more than three replicates.