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Donna Storton, on Moving Princeton s Microarray Lab to New Center

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At A Glance:

  • Donna Storton, Technical Staff, Princeton Microarray Core Lab, Synthesizing and Sequencing Facility, Molecular Biology Department, Princeton University.
  • Education: BS - 1995, 2000, Biochemistry and Exercise Sciences, University of Massachusetts, Amherst.

Donna Storton is the person who gets microarray things done these days at Princeton. She is the chief technician of the school’s core microarray facility, a unit with instruments located in two buildings today, but eventually headed to the $45 million Lewis-Sigler Institute for Integrative Genomics, and its companion Carl Icahn Laboratory, which will be completed under the direction of microarray pioneer David Botstein. (See story p.1).

With a year of experience under her belt, Storton assists researchers in their microarray experiments and then performs the operations such as spotting, hybridization, and imaging. Now she has the opportunity to chip in and help create the microarray processing facility of the future under the direction of Botstein, who will take charge of the center beginning in July.

BioArray News recently talked to Storton about the core facility of the present and that of the future.

 

Tell me about your work.

My job currently has been to develop some microarray projects for various PI’s, and consult —- from start through hybridization — and to print and do some preliminary work prior to printing work. I’m in charge of robotics and the high-throughput work.

Right now, I am personally printing custom orders for four labs, and I’m also consulting on a preliminary library setup for three more labs. There are people who print their own [arrays] — about four of them — and they have done all their preliminary work on their own. As for Affymetrix users, that’s another dozen. There is another PI who has started a project here, and will be moving to Cold Spring Harbor. There are quite a few people in Princeton who are incorporating microarrays into their work. There are biologists, chemists, evolutionary biologists, and geosciences people incorporating microarrays into studies here.

I’m involved in developing our protocols and I consult postdocs in what they want to do, and in the quality of data — but I don’t interpret their data for them.

How did you learn to do this?

I jumped into it. I’ve had some experience with mechanics and robotics and the process work made sense. I’m not willing to say I’m an expert. Whenever you move to a new instrument, it’s a pretty similar process.

Can you describe your lab?

Physically, it’s located in two different labs: It’s in the Lewis Thomas molecular Biology building, and the Moffett Lab for Molecular Biology, which is attached to the Evolutionary Biology and Geosciences building.

We have a homemade spotter, a Gene Machines OmniGrid, and an Affymetrix system. We have two Axon scanners, a 4000A and 4000B, and we are considering acquiring more.

We have a Biomek FX [Beckman Coulter laboratory workstation], which does the high-throughput pipetting. And that helps quite a bit in the preliminary prep and takes a lot of the man hours out of things. One printer has an auto-sampler carousel. The homemade printer is just me, changing plates. I can imagine we will get another printer with another carousel. The carousels hold about 30 plates.

What kind of software do you use?

Most of the users right now write their own scripts. Some use the Axon software for extracting data from the images and write their own scripts to deal with it. They write scripts, some in Perl and some in Java. Some people do use GeneSpring.

We don’t have a database right now, but I believe we will have our own after we get into the new lab.

How close are you to working at full capacity?

At this moment, it’s a one-man team, and I’m close to full capacity. When the new lab is put together, we will be hiring more people. [I] anticipate staffing will at least be tripled, [as] we have several of Dr. Botstein’s people coming in and we are waiting to talk to them about their interim needs. They are going to start their research before the new lab is finished. There are going to be lots and lots of arrays to do.

What will the new facility look like?

We are anticipating having three different areas. An environmentally controlled, close to clean-room type area; and a wet lab; and a small computing area for the scanning and things like that. Researchers will be able to upload their files onto the database and go back to their labs and do their own analysis.

It’s going to be great setting up a very high quality lab. That is going to be a great opportunity. Without that this, the microarray [core] might be piecemeal. Today, I’ve got a little bit of space in one room, and another room and we have scanners in another room. With the new lab, I can spend more time peaking over people’s shoulders to see if they need any more assistance. Their work is only as good as my work, and visa-versa.

What do you think about all this change that is getting ready to come your way?

Really excited about where it’s going. I’ve always enjoyed teaching, so I’m going to enjoy passing this technology to the future users. It’s going to be really a great instrument for research that people are going to be able to include in a lot more studies..

The last job I had was developing a method for an analysis for the exercise science department at the University of Massachusetts. They had a grad student who needed some analysis done. They had done all of the samples collected but they needed a GC mass spec to determine the levels of isotopes that they injected into people so that they could finish the work. All they had was a paper and borrowed GC mass spec. I took it from that, developing all the protocols, analyzing the data for quality, and training future students on the protocols.

Microarrays could be applied to that study, they could have looked for genetic expression changes on top of the other things they were studying, as the samples were already collected.

We are still on the cusp with human chips. The gene sets are still being developed. It’s just waiting for the right time. When the content is available, it’s the right technology.

Tell me a little bit about your microarray network of colleagues.

My network is mostly in industry, including some Affy core directors that I speak with. Affy does a good job of setting up regional meetings for the core directors to get together to discuss problems, pass ideas along. All of us suffer with low budgets and what to do with that. I speak with TeleChem Arrayit — they have pins, spotters and slides that I might like to incorporate into the new facility — and Clontech, which has just released some new automation-friendly products which are very useful. That has made my life a lot easier.

I use some of the Yahoo groups and one at microarray.org. But, right now, I have been the feedback loop here: I try the products, I meet with the vendors, I give each project recommendation based on my experience talking with people, my searches of primary papers. I basically say, this is what I think, you can take it and run with it.

What would you like to see improved in the microarray technology?

Standardization instrument-to-instrument, and program-to-program. But, that is not going to happen, otherwise people wouldn’t make any money.

This technology provides a lot of information that most people don’t have a clue what to do with. We are really trying to make some leaps and bounds with. It would be nice to do an experiment, and look for what you want to look for, put your data up on a database and let someone else look at something else because we can’t do it all by ourselves. It has to be collaborative. A single set of experiments can’t be completely analyzed by even one lab group. It has to be put out and if someone else wants to look at a piece of it, to make sense of it, go right ahead.

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