title: Expression microarrays in plant-virus interaction.
abstract: Since their conception in the late 1990s, microarray techniques have become a tool of choice for monitoring pangenomic gene expression. Although there are a large number of variations on the basic methodology the general approach remains standard and involves the comparison of a "test" RNA with a "control" RNA; in this case "healthy" and "virus-infected" plants. The protocol itself can be broken down into five main parts: RNA extraction, cDNA synthesis, hybridization, array scanning, and data analysis. The method presented is optimized for use with arrays based on glass slides spotted with cDNA, in this case 15,264 cDNAs from Solanum tuberosum. The labeling technique presented involves two steps: hybridization of cDNA produced using oligo-dT linker primers to the array and hybridization with a DNA dendrimer reagent comprising sequence complementary to the linker sequence bound to a fluorescent dye. We also present the use of the R environment for data analysis, generating statistical support for differential gene expression observed.
authors: Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, 1000, Ljubljana, Slovenia.
authors: Kristina
authors: K
authors: Gruden
authors: Marusa
authors: M
authors: Pompe-Novak
authors: Spela
authors: S
authors: Baebler
authors: Hana
authors: H
authors: Krecic-Stres
authors: Natasa
authors: N
authors: Toplak
authors: Matjaz
authors: M
authors: Hren
authors: Polona
authors: P
authors: Kogovsek
authors: Lisa
authors: L
authors: Gow
authors: Gary D
authors: GD
authors: Foster
authors: Neil
authors: N
authors: Boonham
authors: Maja
authors: M
authors: Ravnikar
mesh_terms: D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010942:Plant Viruses / Q000235:genetics*; D010944:Plants / Q000235:genetics* / Q000821:virology*; D018749:RNA, Plant / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant; D004279:DNA, Viral; D018749:RNA, Plant; D012367:RNA, Viral