Multi-Sample Microarrays Sequence Stem Cells 3/30/05
Researchers from The Burnham Institute, San Diego, are using a new microarray technology to perform gene expression profiling on human embryonic stem cells to learn how the cells differentiate into other cell types. The two Sentrix BeadChips from Illumina Inc., San Diego, released this month, enable whole-genome or RefSeq-based expression profiling of multiple samples on the same microarray.
“What we want to do is look at every cell line we can find in the world now, using Illumina’s technology, and build a database of the common gene expression patterns that we note in different populations, and try to discover which of those are attributable to the cells themselves, and which are similar to their spontaneous differentiation,” says Jeanne Loring, PhD, investigator with The Burnham Institute. “This [spontaneous differentiation] is a really big problem with this field right now. People don’t know what they have in their [culture] dishes.”
Loring’s group has been testing Illumina’s array technology as they collect embryonic stem cells from a number of laboratories. For their first experiment, which used Illumina’s microarray analysis technology, they looked at 30 different samples that included six different embryonic stem cell lines, both in undifferentiated and differentiated states. Some of those cells came from the lab of Mahendra Rao, MD, PhD, investigator in the stem cell biology unit, Laboratory of Neurosciences, National Institute on Aging, Bethesda, Md., who had in turn obtained them from several other laboratories around the world, including ones in Israel and Georgia. Other cells Loring worked with were from Wisconsin.
“We had a diverse population of stem cells, and add on top of that the differences in two different labs across the country from each other, with their own ways of doing things,” say Loring. “We put all those together in one experiment, and we got the most remarkable results.”
“We found that all the embryonic stem cells, if you look at their whole gene expression patterns, are very similar to each other. Their differentiated cell types are also very similar to each other.” This was in spite of the differences between her and Rao’s ways of doing things, she says.
“The Illumina technology is inexpensive enough—the first time it’s been inexpensive enough—and it is very robust,” says Loring. Illumina says the pricing can be as low as $100 per sample.
“I’ve been working with arrays for a long time, and I haven’t seen anything like this before,” says Loring. “There are so many data points for each array. For each whole genome, there is an average of 30 replications of the same gene. That gives us tremendous power, and because it’s inexpensive, we have the additional luxury of being able to do triplicates. We get very, very good data.” The goal of The Burnham Institute researchers is to build a database of all the stem cell lines based on this information.
By Elizabeth Tolchin |
