Multiplex Gene Expression HD2 12x135K Microarrays now available from Roche NimbleGen

Roche NimbleGen has launched the NimbleGen Gene Expression 12x135K Microarray, a new multiplex gene expression array on their recently introduced HD2 platform. The 12-plex format offers a cost-effective, high-throughput approach for whole-genome gene expression profiling: Twelve independent samples can be analyzed simultaneously on a single slide. With 135,000 long oligonucleotide probes per array, complete transcriptome coverage is achieved. Similar to the 385K and 4x72K NimbleGen microarrays, the new 12x135K arrays display high specificity, high sensitivity, and excellent reproducibility. There are eight eukaryotic catalog designs available (human, mouse, rat, A. thaliana, C. elegans, D. melanogaster, S. cerevisiae, and S. pombe), all based on the most current whole-genome builds. For researchers interested in studying organisms with genomes that are newly sequenced and annotated, Roche NimbleGen offers the option of a cost-effective custom design.

John Colbourne, Genomics Director at the Center for Genomics and Bioinformatics at Indiana University has been using the HD2 12x135K array to study how populations of the freshwater microcrustacean Daphnia respond to environmental stress. “We begin by validating the current list of genes and improving the gene structure models using NimbleGen tiled expression arrays. The experimental results better delineate transcribed regions of the genome and guide the design of a comprehensive probe set for the 12-plex.” As each array on the 12-plex accommodates 135,000 probes, Colbourne’s group was able to design three probes for every predicted gene and one probe for every transcribed region. “In all, 40% of the designed probes reside in unannotated regions. No other array can easily afford this luxury. In rapid time, our transcription profiling experiments detect the co-regulation of all identified genes and many yet unknown genes under a large range of conditions while simultaneously improving the genome annotation.”

It is the flexible custom design and the excellent quality of gene expression data that sets the 12x135K arrays apart. The multiplex format offers a cost-effective approach without compromising data quality. Licia Selleri, Associate Professor at Cornell University Medical School, confirms that the “use of the NimbleGen 12-plex gene expression microarray is advantageous and more accurate than other platforms because it allows to run replicates within the same array that validate analysis within the same experiment.” Selleri researches the developmental contributions of human proto-oncogenes with a focus on the biological functions of Pbx1, a homeodomain protein originally identified as the product of an oncogene in childhood leukemias. In her lab, they apply a variety of genetic approaches to bridge the gap between gene discovery and gene function. She appreciates the easy functionality of the 12x135K array and the easy interpretation of the data. “Conducting array hybridization is relatively straightforward. The analysis of the results is user-friendly and does not require highly specialized informatics skills”, says Selleri.

The research community has readily recognized the potential of the Roche NimbleGen microarray technology. The arrays are already in use for numerous applications, for instance to study gene expression levels related to multiple signal pathways in tissues and cells. Researchers have also taken advantage of the flexibility of the system to identify factors involved in tissue differentiation and to assess differential gene expression patterns of closely related species. Further potential applications include gene expression studies in cancer and stem cell research, cell differentiation, drug testing, environmental research, and food testing.

“The 12x135K arrays is a powerful tool for accomplishing high throughput gene expression profiling”, says Gerd Maass, President/CEO of Roche NimbleGen. “Combined with NimbleGen custom design option and high probe density, these arrays allow convenient and accurate analysis of a wide range of organisms, from the simplest bacterium to complex mammals and plants. These arrays will accelerate functional genomics research and support our goal of providing innovative solutions for faster and more accurate results.”