Developing the Streptomyces coelicolor microarray

Professor Colin Smith and his group at the University of Surrey worked together with OGT to develop the Streptomyces coelicolor microarray. Prof Smith has been involved in Streptomyces DNA microarrays since 1999, and is funded by the BBSRC and the European Commission to provide Streptomyces DNA microarray resources to researchers throughout the world.

Prof Smith started collaborating with OGT in 2005 to design and develop a high density microarray for ChIP-on-chip analysis of Streptomyces coelicolor. He explained: "The team at OGT has been very interactive, proactive and professional, and it was a true collaboration, with close interaction with the scientists at OGT. We visited their labs and discussed bioinformatics, practical hybridisation work and microarray work. The very high G+C content of the Streptomyces genome creates major challenges for nucleic acid hybridisation so, after OGT’s expert probe design, we experimentally tested almost one million probes, and the bioinformatics team at OGT selected the probes which had the right characteristics of specific signals and sensitivity of signal detection. All the probes on the arrays have been experimentally optimised and validated."

"We were very much involved in the design of the arrays to suit user needs, because we have supplied arrays to about 50 different research groups around the world. Together with OGT, we have come up with a first-in-class array that can be used for ChIP-on-chip, gene expression analysis and CGH, a versatile product that really does advance the field. We have experimentally tested the 4x44k and 2x105k formats and the results are excellent; they are consistent with everything we have done before, but they are giving us far more reproducible and comprehensive data and a much higher resolution picture. The 4x44k would be widely used for most applications, while the 105k gives almost complete coverage of the genome for higher resolution work."

"OGT’s Ink Jet In Situ Synthesis (IJISS) can cost-effectively produce high-density arrays with a quality that is far superior to spotted arrays," continued Prof Smith. "With IJISS technology, it is potentially possible to design a new array on one day, and make it on the following day, making microarray technology much more accessible to all research scientists. The technology is moving so fast, and the days of spotted arrays are numbered. The Streptomyces coelicolor microarray will make microarray technology so much more usable for everybody, and the remarkable consistency of results will allow different groups to be able to compare data. We are expecting major discoveries in the future from meta-analysis of different microarray experiments, and if people are using the same platform, the chances of conducting comprehensive and meaningful meta-analyses are far greater. It really is the next step forward," concluded Prof Smith.