Abstract
Gene expression technology offers great potentials to generate new insights into human disease pathogenesis; however, the data quality remains a major obstacle for realizing its potentials. In the present study 60-mers oligonucleotide target immobilized on coated glass slides were utilized as a model system to investigate parameters, such as target concentration, retention, signal linearity, and fluorescence properties of fluorophores, which likely affect the quality of microarray results. An array calibration slide was used to calibrate an Axon GenePix 4000A scanner and ensure the dynamic range of the instrument. The work is a first step toward our goal of quantitative gene expression measurements.
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References
Mischel, P. S., Cloughesy, T. F., and Nelson, S. F. (2004) DNA-microarray analysis of brain cancer: molecular classification for therapy. Nat. Rev. Neurosci. 5, 782–792.
Chang, J. C., Hilsenbeck, S. G., and Fuqua, S. A. (2005) Genomic approaches in the management and treatment of breast cancer. Br. J. Cancer 92, 618–624.
Kane, M. D., Jatkoe, T. A., Stumpf, C. R., Lu, J., Thomas, J. D., and Madore, S. J. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50 mer) microarrays. Nucleic Acids Res. 28, 4552–4557.
Wang, H., Malek, R. L., Kwitek, A. E., et al. (2003) Assessing unmodified 70-mer oligonucleotide probe performance on galss-slide microarrays. Genome Biol. 4, R5.
Zong, Y., Wang, Y., Zhang, S., and Shi, Y. (2003) How to evaluate a microarray scanner, in Microarrays Methods and Applications—Nuts and Bolts, (Hardiman, G., ed.), DNA Press LLC, pp. 99–114.
Worley, J., Bechtol, K., Penn, S., et al. (2000) A systems approach to fabricating and analyzing DNA microarrays, in Microarray Biochip Technology, (Schena, M., ed.), Eaton Publishing, pp. 65–85.
Basarsky, T., Verdnik, D., Zhai, J. Y., and Wellis, D. (2000) Overview of a microarray scanner: design essentials for an integrated acquisition and analysis platform, in Microarray Biochip Technology, (Schena, M., ed.), Eaton Publishing. pp. 265–284.
Shi, L., Tong, W., Goodsaid, F., et al. (2004) QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev. Mol. Diagn. 4, 761–777.
Gaigalas, A. K., Wang, L., Schwartz, A., Marti, G. E., and Vogt, R. F. (2005) Quantitating fluorescence intensity from fluorophore: assignment of MESF values. J. Res. Natl. Inst. Stand. Technol. 110, 101–114.
Juanita Martinez, M., Aragon, A. M., Rodriguez, A. L., et al. (2003) Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays. Nucleic Acids Res. 31, E18.
Raghavachari, N., Bao, Y. P., Li, G., Xie, X., and Müller, U. R. (2003) Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride. Anal. Biochem. 312, 101–105.
Hessner, M. J., Wang, X., Hulse, K., et al. (2003) Three color cDNA microarrays: quantitative assessment through the use of fluorescein-labeled probes. Nucleic Acids Res. 31, E14.
Hessner, M. J., Meyer, L., Tackes, J., Muheisen, S., and Wang, X. (2004) Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics 5, 53.
Yue, H., Scott Eastman, P., Wang, B. B., et al. (2001) An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res. 29, E41.
Battaglia, C., Salani, G., Consolandi, C., Rossi Bernardi, L., and De Bellis, G. (2000) Analysis of DNA microarrays by non-destructive fluorescent staining using SYBR green II. Biotechniques 29, 78–81.
Ramdas, L., Coombes, K. R., Baggerly, K., et al. (2001) Sources of nonlinearity in cDNA microarray expression measurements. Genome Biol. 2, R47.
Wang, L., Gaigalas, A. K., and Reipa, V. (2005) Optical properties of Alexa™ 488 and Cy™ 5 immobilized on a glass surface. Biotechniques 38, 127–132.
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© 2007 Humana Press Inc., Totowa, NJ
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Wang, L., Gaigalas, A.K., Satterfield, M.B., Salit, M., Zong, Y., Noble, J. (2007). Evaluating the Quality of Data From Microarray Measurements. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology™, vol 381. Humana Press. https://doi.org/10.1007/978-1-59745-303-5_6
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DOI: https://doi.org/10.1007/978-1-59745-303-5_6
Publisher Name: Humana Press
Print ISBN: 978-1-58829-589-7
Online ISBN: 978-1-59745-303-5
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