title: Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection.
abstract: BACKGROUND
  Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe-set, consisting of up to 16 probe-pairs. Signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. We have previously developed a technique to study the transcriptomes of heterologous species based on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology.
  
  
  RESULTS
  Here we have investigated the effects of hybridising homologous species gDNA to study the transcriptomes of species for which the arrays have been designed. Genomic DNA from Arabidopsis thaliana and rice (Oryza sativa) were hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively. Probe selection based on gDNA hybridisation intensity increased the number of genes identified as significantly differentially expressed in two published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice.
  
  
  CONCLUSIONS
  This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays.
authors.affiliation: Plant Science Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK. neil@arabidopsis.info
authors.forename: Neil S
authors.initials: NS
authors.lastname: Graham
authors.forename: Martin R
authors.initials: MR
authors.lastname: Broadley
authors.forename: John P
authors.initials: JP
authors.lastname: Hammond
authors.forename: Philip J
authors.initials: PJ
authors.lastname: White
authors.forename: Sean T
authors.initials: ST
authors.lastname: May
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D015342:DNA Probes; D015870:Gene Expression; D016678:Genome; D018745:Genome, Plant; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics; D012313:RNA / Q000235:genetics; D012641:Selection, Genetic; D014158:Transcription, Genetic
chemical_list: D015342:DNA Probes; D012313:RNA