AT A GLANCE Ph.D. in biology from the University of Texas at Austin in 1984. Research interests center on using microarrays to examine microbes in the environment. Interests: Remodeling homes, reading.
QWhat do you like most about the microarray field?
AAt the moment what I like more than anything is the potential to have a global view of a particular point in a gene expression profile.
QWhat role do microarrays play in research at the University of Cincinnati?
AMainly we do gene expression. UC is fairly large in cardiac research, so there is quite a bit of [gene expression] research looking at different disease states in cardiac research. There is also research looking at the effects of toxicants on affected vs. unaffected tissues, as well as some developmental research comparing gene expression profiles at different stages in different tissues.
QWhat types of arrays do you use and in what combination?
AWe print our own arrays, and have two libraries we concentrate on, human and mouse. We also print custom-made libraries.
QHow is the microarray facility set up within the university?
AThe Genomics and Microarray Laboratory is a nonprofit setup, and is located within the UC Medical Center. It is available to all investigators in the UC system. Arrays are available at cost to researchers, and prices for outside researchers are somewhat higher.
We handle the entire process except for isolating the RNA, which the investigator has to do. We have PCR products and are about to buy an oligo library. We do the washing, labeling, and the first pass analysis, where we make sure that the experiment worked well, then export the data to the bioinformatics core. If the experiment didn’t work it’s often an RNA problem. We have an Agilent bioanalyzer 2100 that can load RNA in a matter of minutes, and get a ratio. And looking at the profile and the ratios, you can determine whether it’s good or not.
QWhat’s the bottleneck once you get the good RNA?
AThe RNA labeling stage. We can do six or eight slides a day, and sometimes it piles up.
QHave you developed any special arraying protocols?
AWe have worked out most of the steps for getting fine, reliable, and consistent results using printed oligos. We are putting them on our website, at http://microarray.uc.edu/ Resources/protocols.htm.
QWhat kind of arrayer do you use?
AWe use a GeneMachines OmniGrid, which works fine.
QWhat methods do you use to analyze microarray data?
AWe use the Axon GenePix software, and then export it to the bioinformatics core, where they use GeneSpring.
QWhat is the biggest challenge you face in working with microarrays?
ARefining the technology to a point where it’s repeatable and you can validate the data, because even with a one percent error, if you are looking at 10,000 spots that means 100 false positives. We are always trying to eliminate any variability between slides and experiments. The big thing in the field right now is trying to get a handle on the best controls and data analysis methods to look at this huge volume of data. We’re all striving for consistency.
QWhat bits of advice would you give to a colleague who is setting up and running a core microarray facility?
AIt may be more art than science at this point. What may work for someone else doesn’t always work for you. There are definitely pitfalls and the details can kill you. The biggest challenge is consistently labeling the RNA. The better the RNA, the better results. Since the investigator is generating the RNA, it’s always a challenge to keep the RNA quality up.
QIf you could make out a wish list for microarray technology advances or improvements over the next couple of years, what do you most want or need?
AIt would be, again, a final determination of a working methodology for the best way to analyze these data using an agreed upon set of controls.