%0 Journal Article
%T A flexible whole-genome microarray for transcriptomics in three-spine stickleback (Gasterosteus aculeatus)
%A Erica H Leder
%A Juha Meril£¿
%A Craig R Primmer
%J BMC Genomics
%D 2009
%I BioMed Central
%R 10.1186/1471-2164-10-426
%X We designed 43,392 unique oligonucleotide probes representing 19,274 genes (93% of the estimated total gene number), and tested the hybridization performance of both DNA and RNA from different populations to determine the efficacy of probe design for transcriptome analysis using the Agilent array platform. The majority of probes were functional as evidenced by the DNA hybridization success, and 30,946 probes (14,615 genes) had a signal that was significantly above background for RNA isolated from liver tissue. Genes identified as being expressed in liver tissue were grouped into functional categories for each of the three Gene Ontology groups: biological process, molecular function, and cellular component. As expected, the highest proportions of functional categories belonged to those associated with metabolic functions: metabolic process, binding, catabolism, and organelles.The probe and microarray design presented here provides an important step facilitating transcriptomics research for this important research organism by providing a set of over 43,000 probes whose hybridization success and specificity to liver expression has been demonstrated. Probes can easily be added or removed from the current design to tailor the array to specific experiments and additional flexibility lies in the ability to perform either one-color or two-color hybridizations.Microarrays and other whole genome methods are increasingly being applied to examine transcription patterns relevant for ecology and evolution in wild populations (e.g[1,2]). One of the obstacles to applying this technology to non-model organisms is sufficient sequence data from which array features can be designed. Because of this, many of the arrays used for non-model organisms have been cDNA arrays spotted from cDNA clones since whole-genome sequence information does not exist (e.g[1,3]). This limits the number of genes to those found in cDNA libraries which may not be representative of the whole genome. Additionall
%U http://www.biomedcentral.com/1471-2164/10/426