Microarray Research Facility

Introduction

Personnel/Contact Us

Experimental Design

RNA Needed

RNA Quality

Frequently Asked Questions

Bioinformatics

Equipment

Protocols

Publications

Oklahoma Microarray INBRE Labs

Other Core Facilities

Experimental Design for Microarray Studies
All projects at OMRF's Microarray Research Facility begin by consulting our operations and bioinformatics staff to optimize the design of proposed microarray experiments. Microarrays are extremely sensitive in their ability to distinguish differences in levels of transcripts. Such differences arise from biological variations among subjects, experimental variations between groups, and technical differences in the way samples are prepared. One aim of optimizing the design of experiments is to reduce technical variations in order to distinguish biologically meaningful differences between groups. RNA molecules transcribed from different genes have considerably different half-lives. For this reason, researchers should process samples in parallel using identical methods. Tissues and cells should be kept under identical conditions during processing. If possible, the same person should prepare all samples for microarrays to be compared. Once all samples for a given experiment are received at our facility, we will analyze the quality of RNA for degradation using capillary gel electrophoresis. Labeling and hybridizations of samples with good quality RNA will then be performed in parallel and the results analyzed. Users should refer to descriptions of RNA quantity and quality on our web site.

Discussions to optimize the experimental design will also include the number of biologic replicates needed to achieve sufficient statistical power for data analysis. In general, our methods have sufficient power to discriminate two-fold, statistically significant differences in gene expression using a minimum of 5 biological replicates between groups with limited intragroup heterogenity. Such heterogenity is frequently encountered in experiments using cultured cell lines. Additional samples are needed when sample heterogeneity is known or suspected, as is common in human diseases and certain experimetal animal models. Users are encouraged to collect a few additional samples at the time of the experiment in the event that RNA is degraded in a particular sample or to remove technical artifacts that may limit the ability to acquire microarray data from certain samples. For longitudinal/time course studies, the number of replicates needed depends on the number of time points being analyzed. For all of these reasons, it is necessary for individuals who are considering running microarrays in our facility to discuss technical and statistical aspects of the design of their experiments BEFORE the experiment is performed.