Abstract
Microarray analyses provide information on the relative expression levels of large numbers of gene products (transcripts). As such they have been widely used to examine differences in gene expression across a variety of samples such as tissues and life-cycle stages. Due to a previous lack of sequence data, microarray analyses have typically centred on the study of well-characterised model organisms. However, the recent availability of large sets of expressed sequence tags (ESTs) generated for the purpose of gene discovery offers the opportunity to consider designing and applying microarray technology to a larger and more diverse set of species. Here we outline the array-design process involving the generation of an optimised set of oligoprobes from a minimally redundant but maximally representative list of sequences from raw EST data. We illustrate these principles by showing how we designed and fabricated a high-density oligoarray for the rainbow trout, a non-model species for which large numbers of ESTs, and a non-redundant assembly is available. This approach brings array technology within the reach of all investigators, even those with limited budgets.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hughes, T. R., Mao, M., Jones, A. R., Burchard, J., Marton, M. J., Shannon, K. W., Lefkowitz, S. M., Ziman, M., Schelter, J. M., Meyer, M. R., Kobayashi, S., Davis, C., Dai, H., He, Y. D., Stephaniants, S. B., Cavet, G., Walker, W. L., West, A., Coffey, E., Shoemaker, D. D., Stoughton, R., Blanchard, A. P., Friend, S. H., and Linsley, P. S. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol. 19, 342–47.
Gracey, A. Y., Troll, J. V., and Somero, G. N. (2001) Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc Natl Acad Sci USA 98, 1993–8.
Podrabsy, J., and Somero, G. (2004) Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J Exp Biol 207, 2237–54.
Carninci, P., Shibata, Y., Hayatsu, N., Sugahara, Y., Shibata, K., Itoh, M., Konno, H., Okazaki, Y., Muramatsu, M., and Hayashizaki, Y. (2000) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res 10, 1617–30.
Sagerstrom, C. G., Sun, B. I., and Sive, H. L. (1997) Subtractive cloning : Past; present; and future. Ann Rev Biochem 66, 751–83.
Diatchenko, L., Lau, Y. F., Campbell, A. P., Chenchik, A., Moqadam, F., Huang, B., Lukyanov, S., Lukyanov, K., Gurskaya, N., Sverdlov, E. D., and Siebert, P. D. (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93, 6025–30.
Diatchenko, L., Lukyanov, S., Lau, Y. F. C., and Siebert, P. D. (1999) Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes. Methods Enzymol 303, 349–80.
Leparc, G. G., Tu¨chler, T., Striedner, G., Bayer, K., Sykacek, P., Hofacker, I. P., and Kreil, D. P. (2008) Model-based probe set optimization for high-performance microarrays. Nucleic Acids Res. doi:10.1093/nar/gkn1001
Kreil, D., Russell, R., and Russell, S. (2006) Microarray oligonucleotide probes. Methods Enzymol 410, 73–98.
Charbonnier, Y., Gettler, B., Francois, P., Bento, M., Renzoni, A., Vaudaux, P., Schlegel, W., and Schrenzel, J. (2005) A generic approach for the design of whole-genome oligoarrays, validated for genotyping, deletion mapping and gene expression analysis on Staphylococcus aureus. BMC Genomics 6, 95.
Stenberg, J., Nilsson, M., and Landegren, U. (2005) ProbeMaker: an extensible framework for design of sets of oligonucleotide probes. BMC Bioinformatics 6, 229.
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2006) GenBank. Nucleic Acids Res 1, D16–D20.
Maglott, D., Ostell, J., Pruitt, K. D., and Tatusova, T. (2005) Entrez gene: gene-centered information at NCBI. Nucleic Acids Res 1, D54–D8.
Gerhard, D., Wagener, L., Feingold, E., Shenman, C., Grouse, L., Schuler, G., Klein, S., DOld, S., Rasooly, R., and Good, P. (2004) The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res 41, 2121–27.
Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Natale, D. A., O'Donovan, C., Redaschi, N., and Yeh, L.S. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 1, D115–D19.
Dai, H., Meyer, M., Stepanients, S., Ziman, M., and Stoughton, R. (2002) Use of hybridisation kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Res 30, e86.
Churchill, G. (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32, 490–5.
Wit, E., and McClure, J. (2004) Statistics for Microarrays: design, Analysis and Inference. Wiley Interscience, New York.
Speed, T. (Ed.) (2003) Statistical Analysis of Gene Expression Microarray Data. CRC Press, Chaman & Hall, Boca Raton.
Quackenbush, J. (2001) Computational analysis of microarray data. Nat Rev Genet 2, 418–27.
Churchill, G. A. (2004) Using ANOVA to analyze microarray data. Biotechniques 37, 173–75.
Berger, J., Hautaniemi, S., Järvinen, A.-K., Edgren, H., Mitra, S., and Astola, Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics 5, 194.
Sutton, G. G., White, O., Adams, M. D. and Kerlavage, A. R. (1995) TIGR Assembler: a New Tool for Assembling Large Shotgun Sequencing Projects. Genome Sci Technol 1, 9–19.
Wheeler, D. L., Church, D. M., Federhen, S., Lash, A. E., Madden, T. L., Pontius, J. U., Schuler, G. D., Schriml, L. M., Sequeira, E., Tatusova, T. A., and Wagner, L. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res 31, 28–33.
Rouillard, J. M., Zuker, M., and Gulari, E. (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach Nucleic Acids Res 31, 3057–62.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Li, W., Olohan, L., Williams, D., Hughes, M., Gracey, A., Cossins, A. (2009). Application of ESTs in Microarray Analysis. In: Parkinson, J. (eds) Expressed Sequence Tags (ESTs). Methods in Molecular Biology, vol 533. Humana Press. https://doi.org/10.1007/978-1-60327-136-3_14
Download citation
DOI: https://doi.org/10.1007/978-1-60327-136-3_14
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-58829-759-4
Online ISBN: 978-1-60327-136-3
eBook Packages: Springer Protocols