%0 Journal Article
%T Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection
%A Neil S Graham
%A Martin R Broadley
%A John P Hammond
%A Philip J White
%A Sean T May
%J BMC Genomics
%D 2007
%I BioMed Central
%R 10.1186/1471-2164-8-344
%X 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.This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays.The use of microarrays to determine global transcriptional profiles is a valuable and widely-used tool for understanding the regulation of biological systems [1,2]. Several microarray platforms are used for these studies, including spotted arrays (using cDNAs, PCR products or oligonucleotides) and in situ synthesised arrays including Agilent SurePrint and Affymetrix GeneChip arrays. GeneChip arrays have a number of advantages over other arrays. For example, the uniformity and reproducibility of data from GeneChip arrays facilitates the curation of large data sets and subsequent inter-experimental comparisons [1-5]. Each gene depicted on a GeneChip array is represented by up to 16 probe-pairs, with each probe-pair consisting of a 25 base oligo perfect-match (PM) probe, designed to bind perfectly to the gene sequence, and a 25 base oligo mis-match (MM) probe, which contains a mis-match base at the 13th base position, designed to measure non-specific binding [1]. This contrasts with the single cDNA or oligo probe used to assay a gene on most other arrays. However, since several signal values are generated for each gene, it is more complex to produce a single expression value for each gene, as probes within a probe-set may not have similar signal intens
%U http://www.biomedcentral.com/1471-2164/8/344