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Global mRNA changes in microarray experiments

Nature Biotechnology volume 26, pages 741–742 (2008)Cite this article

To the editor:

Microarray mRNA expression profiling is of wide utility in all areas of the life sciences1,2. Almost all normalization algorithms used to interpret microarray experiments calculate changes in transcript abundance based on the assumption that no changes occur in the total amount of mRNA. This assumption is, however, violated under many experimental conditions, often resulting in the false classification of thousands of genes as differentially expressed3. The potential for environmental and developmental effects on global mRNA have been demonstrated for heat shock and serum deprivation in mammalian cells and yeast stationary phase, respectively3. In addition, two papers4,5 published in a previous issue from the MicroArray Quality Control (MAQC) project highlighted the potential for tissue-specific changes, reporting global mRNA differences between human universal reference and brain RNA samples. Here, we present a simple method to generate external controls for Affymetrix (Santa Clara, CA, USA) GeneChip oligonucleotide microarrays to allow these platforms to measure absolute mRNA expression at the global level.

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Figure 1: Use of external RNA controls.

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Acknowledgements

We thank Melanie Krämer for help harvesting plant material, the RZPD for array hybridization and Alisdair Fernie and Matthias Steinfath for useful comments on the manuscript.

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Author notes

  1. Matthew A Hannah

    Present address: Present address: Bayer Cropscience N.V., Technologiepark 38, 9000 Gent, Belgium.,

Authors and Affiliations

  1. Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, D-14424, Germany

    Matthew A Hannah, Henning Redestig, Andrea Leisse & Lothar Willmitzer

Authors
  1. Matthew A Hannah
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  2. Henning Redestig
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  3. Andrea Leisse
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  4. Lothar Willmitzer
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Contributions

M.A.H. conceived and supervised the study, performed the experiments and analyzed data. H.R. analyzed data and developed the normalization. A.L. prepared samples for expression profiling. L.W. discussed the project and provided group support and supervision. M.A.H., H.R. and L.W. wrote the manuscript.

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Figures 1,2, Table 1, Methods, Results and Discussion (PDF 1044 kb)

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Hannah, M., Redestig, H., Leisse, A. et al. Global mRNA changes in microarray experiments. Nat Biotechnol 26, 741–742 (2008). https://doi.org/10.1038/nbt0708-741

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