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A comparative analysis of transcript abundance using SAGE and Affymetrix arrays

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Abstract

A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of “genes” and these are discussed.

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Acknowledgements

This work was supported by the Food Standards Agency in the UK (GO2) and a BBSRC ISIS award and a McKnight Landgrant Professorship to Dr. Gary Muehlbauer. The HarvEST database was kindly provided by Drs. Tim Close and Steve Wanamaker, UCR. We thank Ilze Druka for advice on data analysis and Arnis Druka for useful discussions about this work.

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Authors and Affiliations

  1. Genome Dynamics, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    Adel F. M. Ibrahim & Robbie Waugh

  2. Gene Expression, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    Peter E. Hedley

  3. Computational Biology, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    Linda Cardle & David F. Marshall

  4. Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN, 55108, USA

    Warren Kruger & Gary J. Muehlbauer

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  1. Adel F. M. Ibrahim
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  2. Peter E. Hedley
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  3. Linda Cardle
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  4. Warren Kruger
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  5. David F. Marshall
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  6. Gary J. Muehlbauer
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  7. Robbie Waugh
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Correspondence to Robbie Waugh.

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Ibrahim, A.F.M., Hedley, P.E., Cardle, L. et al. A comparative analysis of transcript abundance using SAGE and Affymetrix arrays. Funct Integr Genomics 5, 163–174 (2005). https://doi.org/10.1007/s10142-005-0135-4

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  • DOI: https://doi.org/10.1007/s10142-005-0135-4

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