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Properties of signal intensities observed with individual probes of GeneChip Rat Gene 1.0 ST Array, an affymetric microarray system

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Abstract

For proper evaluation of the results of microarray experiments, it is important to understand how the signal intensities of individual probes are determined. Our previous studies revealed that signal intensities of individual probes in the Agilent array system (code G4131F) are largely dependent upon the location of the probes in the mRNA. In the present study, we examined the properties of signal intensities of individual probes in an Affymetrix array system (GeneChip Rat Gene 1.0 ST Array), in which a random primer fused to the T7 promoter sequence is employed. Distinct from the Agilent array system, individual probes used in this Affymetrix array system did not show the probe-location effects, but gave relatively diverse signal intensities. However, the diversities of the signal intensities of these individual probes were not due to experimental error.

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Authors and Affiliations

  1. Institute for Genome Research, University of Tokushima, Kuramotocho-3, Tokushima, 770-8503, Japan

    Eriko Obana, Takuya Hada, Takenori Yamamoto, Rei Kakuhata & Yasuo Shinohara

  2. Faculty of Pharmaceutical Science, University of Tokushima, 1-78 Shomachi-1, Tokushima, 770-8505, Japan

    Eriko Obana, Takuya Hada & Yasuo Shinohara

  3. Radioisotope Research Center, University of Tokushima, Kuramotocho-3, Tokushima, 770-8503, Japan

    Takuya Saze, Hirokazu Miyoshi & Yasuo Shinohara

  4. Japan Bioindustry Association, Hatchobori-2, Chuo-ku, Tokyo, 104-0032, Japan

    Tomoshige Hori

Authors
  1. Eriko Obana
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  2. Takuya Hada
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  3. Takenori Yamamoto
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  4. Rei Kakuhata
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  5. Takuya Saze
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  6. Hirokazu Miyoshi
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  7. Tomoshige Hori
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  8. Yasuo Shinohara
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Corresponding author

Correspondence to Yasuo Shinohara.

Additional information

Eriko Obana and Takuya Hada have contributed equally to this study.

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Obana, E., Hada, T., Yamamoto, T. et al. Properties of signal intensities observed with individual probes of GeneChip Rat Gene 1.0 ST Array, an affymetric microarray system. Biotechnol Lett 34, 213–219 (2012). https://doi.org/10.1007/s10529-011-0776-4

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  • DOI: https://doi.org/10.1007/s10529-011-0776-4

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