Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection

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Graham, Neil S. ; Broadley, Martin R. ; Hammond, John P. ; White, Philip J. ; May, Sean T. (2007)

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\ud have previously developed a technique to study the transcriptomes of heterologous species based\ud on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology.\ud 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\ud intensity increased the number of genes identified as significantly differentially expressed in two\ud published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice.\ud Conclusion: This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays.
  • References (33)
    33 references, page 1 of 4

    1. Lipschutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ: High density synthetic oligonucleotide arrays. Nature Genetics 1999, 21:20-24.

    2. Henning L, Menges M, Murray JA, Gruissem W: Arabidopsis transcript profiling on Affymetrix GeneChip arrays. Plant Molecular Biology 2003, 53:457-465.

    3. Zhu T, Wang X: Large scale profiling of the Arabidopsis transcriptome. Plant Physiology 2000, 124:1472-1476.

    4. Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S: NASCArrays: A repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Research 2004, 32:D575-D577.

    5. Redman RD, Schwartz C, Morel JL, Edmondson J: Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant Journal 2004, 38:545-561.

    6. Grigoryev DM, Ma S-F, Simon BA, Irizarrt RA, Ye SQ, Garcia JGN: In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip® technology. BMC Genomics 2005, 6:62.

    7. Seo J, Hoffman EP: Probe-set algorithms: Is there a rational best bet? BMC Bioinformatics 2006, 7:395.

    8. Affymetrix Microarray Suite User Guide [http://www.affyme trix.com/support/technical/manuals.affx]

    9. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proceedings of the National Academy of Sciences of the United States of America 2001, 98:31-36.

    10. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: design issues and standard error application. Genome Biology 2001, 2:0032.1-0032.11.

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