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Benchmarking the CATMA microarray : a novel tool for Arabidopsis transcriptome analysis

(2005) PLANT PHYSIOLOGY. 137(2). p.588-601
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Abstract
Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags of 150 to 500 bp, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (The Institute for Genomic Research release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled targets derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range, presumably because signal saturation occurred for transcripts at concentrations beyond 1,000 copies per cell. Sensitivity was comparable for all three platforms. For Affymetrix GeneChip data, the RMA software package outperformed Microarray Suite 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value. In addition, taking advantage of replicates in our dataset, we conducted a robust statistical analysis of the platform propensity to yield false positive and false negative differentially expressed genes, and all gave satisfactory results. The results establish the CATMA array as a mature alternative to the Affymetrix and Agilent platforms.
Keywords
REVEALS, DISCOVERY, PROFILES, ARRAY, PLATFORMS, METAANALYSIS, OLIGONUCLEOTIDE, SEQUENCE TAGS, GENE-EXPRESSION, FUNCTIONAL GENOMICS

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Chicago
Allemeersch, Joke, Steffen Durinck, Rudy Vanderhaeghen, Philippe Alard, Ruth Maes, Kurt Seeuws, Tom Bogaert, et al. 2005. “Benchmarking the CATMA Microarray : a Novel Tool for Arabidopsis Transcriptome Analysis.” Plant Physiology 137 (2): 588–601.
APA
Allemeersch, J., Durinck, S., Vanderhaeghen, R., Alard, P., Maes, R., Seeuws, K., Bogaert, T., et al. (2005). Benchmarking the CATMA microarray : a novel tool for Arabidopsis transcriptome analysis. PLANT PHYSIOLOGY, 137(2), 588–601.
Vancouver
1.
Allemeersch J, Durinck S, Vanderhaeghen R, Alard P, Maes R, Seeuws K, et al. Benchmarking the CATMA microarray : a novel tool for Arabidopsis transcriptome analysis. PLANT PHYSIOLOGY. 2005;137(2):588–601.
MLA
Allemeersch, Joke, Steffen Durinck, Rudy Vanderhaeghen, et al. “Benchmarking the CATMA Microarray : a Novel Tool for Arabidopsis Transcriptome Analysis.” PLANT PHYSIOLOGY 137.2 (2005): 588–601. Print.
@article{331327,
  abstract     = {Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags of 150 to 500 bp, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (The Institute for Genomic Research release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled targets derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range, presumably because signal saturation occurred for transcripts at concentrations beyond 1,000 copies per cell. Sensitivity was comparable for all three platforms. For Affymetrix GeneChip data, the RMA software package outperformed Microarray Suite 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value. In addition, taking advantage of replicates in our dataset, we conducted a robust statistical analysis of the platform propensity to yield false positive and false negative differentially expressed genes, and all gave satisfactory results. The results establish the CATMA array as a mature alternative to the Affymetrix and Agilent platforms.},
  author       = {Allemeersch, Joke and Durinck, Steffen and Vanderhaeghen, Rudy and Alard, Philippe and Maes, Ruth and Seeuws, Kurt and Bogaert, Tom and Coddens, Kathleen and Deschouwer, Kirsten and Van Hummelen, Paul and Vuylsteke, Marnik and Moreau, Yves and Kwekkeboom, Jeroen and Wijfjes, Andr{\'e} HM and May, Sean and Beynon, Jim and Hilson, Pierre and Kuiper, Martin},
  issn         = {0032-0889},
  journal      = {PLANT PHYSIOLOGY},
  language     = {eng},
  number       = {2},
  pages        = {588--601},
  title        = {Benchmarking the CATMA microarray : a novel tool for Arabidopsis transcriptome analysis},
  url          = {http://dx.doi.org/10.1104/pp.104.051300},
  volume       = {137},
  year         = {2005},
}

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