Abstract
DNA microarrays are widely used to analyze genome-wide gene expression patterns and to study genotypic variations. They are miniaturized collections of thousands of DNA fragments arrayed on a surface. Based on nucleic acid complementary binding, they serve as a tool to interrogate complex populations of nucleic acids for abundance or binding affinity of particular sequences. Before a nucleic acid (target) can be used for hybridization to the probes of a microarray, it needs to be extracted from the tissue and labeled. Frequently, it also needs to be amplified to increase detection sensitivity. During a hybridization process, labeled target molecules with sequences complementary to the probes are captured quantitatively. Subsequently, a reader measures the amount of label on each probe. To generate accurate and informative data, one of the most critical aspects of these experiments is the quality of both the isolated and the labeled nucleic acid samples. This chapter describes detailed procedures for the preparation of labeled RNA samples for DNA microarray analysis.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.
Lipshultz, R. J., Fodor, S. P. A., Gingeras, T. R., and Lockhart,. J. High density synthetic oligonucleotide arrays. Nat. Genet. 21s, 20–24.
Borevitz, J. O., Liang, D., Plouffe, D., et al. (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res. 13, 513–523.
Aharoni, A. and Vorst, O. (2002) DNA microarrays for functional plant genomics. Plant Mol. Biol. 48, 99–118.
Donson, J., Fang, Y., Espiritu-Santo, G., et al. (2002) Comprehensive gene expression analysis by transcript profiling. Plant Mol. Biol. 48, 75–97.
Mele, G. and Hake, S. (2003) Expression profiling of plant development. Genome Biol. 4, 215.
Zhu, T. (2003) Global analysis of gene expression using GeneChip microarrays. Curr. Opin. Plant Biol. 6, 418–425.
Khandurina, J., Chang, H.-S., Wanders, B., and Guttman, A. (2002) Automated high-throughput RNA analysis by capillary electrophoresis. Bio Techniques 32, 1226–1230.
Zarrinkar, P. P., Mainquist, J. K., Zamora, M., et al. (2001) Arrays of arrays for high-throughput gene expression profiling. Genome Res. 11, 1256–1261.
Zhu, T., Chang, H.-S., Schmeits, J., et al. (2001) Gene expression microarrays: improvements and applications towards agricultural gene discovery. J. Assoc. Lab. Automat. 6, 95–98.
Hertzberg, M., Sievertzon, M., Aspeborg, H., Nilsson, P., Sandberg, G., and Lundeberg, J. (2001) cDNA microarray analysis of small plant tissue samples using a cDNA tag target amplification protocol. Plant J. 25, 585–591.
Nakazono, M., Qiu, F., Borsuk, L. A., and Schnable, P. S. (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 15, 583–596.
Affymetrix. (2003) GeneChip® Expression Analysis Technical Manual. http://www.affymetrix.com/support/technical/manuals.affx.
Zhu, T. and Wang, X. (2000) Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol. 124, 1472–1476.
Zhu, T., Budworth, P., Han, B., Brown, D., Chang, H.-S., Zou, Z., and Wang, X. (2001) Towards elucidating global gene expression in developing Arabidopsis: parallel analysis of 8300 genes. Plant Physiol. Biochem. 39, 221–242.
Eisen, M. B. and Brown, P. O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol. 303, 179–205.
Chang, S., Puryear, J., and Cairney, J. (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11, 113–116.
Tepperman, J. M., Zhu, T., Chang, H. S., Wang, X., and Quail, P. H. (2001) Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc. Natl. Acad. Sci. USA 98, 9437–9442.
Chomczynski, P. and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156–159.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc.
About this protocol
Cite this protocol
Zhu, T., Chang, S.H., Gil, P. (2006). Target Preparation for DNA Microarray Hybridization. In: Salinas, J., Sanchez-Serrano, J.J. (eds) Arabidopsis Protocols. Methods in Molecular Biology™, vol 323. Humana Press. https://doi.org/10.1385/1-59745-003-0:349
Download citation
DOI: https://doi.org/10.1385/1-59745-003-0:349
Publisher Name: Humana Press
Print ISBN: 978-1-58829-395-4
Online ISBN: 978-1-59745-003-4
eBook Packages: Springer Protocols