Overview of Nucleic Acid Arrays

Joseph DeRisi1

1 University of California, San Francisco, San Francisco, California
Publication Name:  Current Protocols in Neuroscience
Unit Number:  Unit 4.25
DOI:  10.1002/0471142301.ns0425s16
Online Posting Date:  November, 2001
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Nucleic acid array technology refers to the use and fabrication of arrays containing thousands of nucleic acid samples bound to solid substrates such as glass microscope slides or silicon wafers. Because the physical area occupied by each sample is usually 50 to 200 micrometers in diameter, it is possible to assay nucleic acid samples representing entire genomes, ranging in size from 3,000 to 32,000 genes, on a single slide. Microarrays are useful for analyzing gene expression patterns, genotyping and genetic mapping, comparative genomic hybridization, polysome analysis, and DNA‚Äźprotein interactions. This overview describes the technology and applications, and provides valuable web site listings for obtaining additional information.

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Table of Contents

  • What are Microarrays Good for?
  • What Else are Nucleic Acid Microarrays Good for?
  • What About Data Analysis?
  • Where Can I Get More Information?
  • Literature Cited
  • Figures
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PDF or HTML at Wiley Online Library



Literature Cited

Literature Cited
   Alizadeh, A., Eisen, M., Botstein, D., Brown, P.O., and Staudt, L.M. 1998. Probing lymphocyte biology by genomic‐scale gene expression analysis. J. Clin. Immunol. 18:373‐379.
   Amundson, S.A., Bittner, M., Chen, Y., Trent, J., Meltzer, P., and Fornace, A.J.Jr. 1999. Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses. Oncogene 18:3666‐3672
   Bassett, ,D.E. Jr., Eisen, M.B., and Boguski, M.S. 1999. Gene expression informatics—it's all in your mine. Nature Genet. 21:51‐55.
   Behr, M.A., Wilson, M.A., Gill, W.P., Salamon, H., Schoolnik, G.K., Rane, S., and Small, P.M. 1999. Comparative genomics of BCG vaccines by whole‐genome DNA microarray. Science 284:1520‐1523.
   Brown, P.O. and Botstein, D. 1999. Exploring the new world of the genome with DNA microarrays. Nature Genet. 21:33‐37.
   Cheung, V.G., Gregg, J.P., Gogolin‐Ewens, K.J., Bandong, J., Stanley, C.A., Baker, L., Higgins, M.J., Nowak, N.J., Shows, T.B., Ewens, W.J., Nelson, S.F., and Spielman, R.S. 1998. Linkage‐disequilibrium mapping without genotyping. Nature Genet. 18:225‐230.
   Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., and Davis, R.W. 1998. A genome‐wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2:65‐73.
   Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O., and Herskowitz, I. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699‐705.
   DeRisi, J.L., Iyer, V.R., and Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680‐686.
   Diehn, M., Eisen, M., Brown, P., and Botstein, D. 2000. Large‐scale identification of membrane‐associated gene products using DNA microarrays. Nature Genet. 25:58‐62.
   Eberwine, J. 1996. Amplification of mRNA populations using aRNA generated from immobilized oligo(dT)‐T7 primed cDNA. Biotechniques 20:584‐591.
   Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome‐wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95:14863‐14868.
   Ferea, T.L., Botstein, D., Brown, P.O., and Rosenzweig, R.F. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U.S.A. 96:9721‐9726.
   Fodor, S.P., Read, J.L., Pirrung, M.C., Stryer, L., Lu, A.T., and Solas, D. 1991. Light‐directed, spatially addressable parallel chemical synthesis. Science 251:767‐773.
   Hacia, J.G., Brody, L.C., Chee, M.S., Fodor, S.P., and Collins, F.S. 1996. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two‐colour fluorescence analysis. Nature Genet. 14:441‐447.
   Hayward, R., DeRisi, J., Alfadhli, S., Kaslow, D., Brown, P., and Rathod, P. 2000. Shotgun DNA microarrays and stage‐specific gene expression in Plasmodium falciparum malaria. Mol. Microbiol. 35:6‐14.
   Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G.T., Moore, J.C., Lee, F., Trent, J.M., Staudt, L.M., Hudson, J. Jr., Boguski, M.S., Lashkari, D., Shalon, D., Botstein, D., and Brown, P.O. 1999. The transcriptional program in the response of human fibroblasts to serum. Science 283:83‐87.
   Kallioniemi, A., Kallioniemi, O.P., Sudar, D., Rutovitz, D., Gray, J.W., Waldman, F., and Pinkel, D. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818‐821.
   McAllister, L., Penland, L., and Brown, P.O. 1998. Enrichment for loci identical‐by‐descent between pairs of mouse or human genomes by genomic mismatch scanning. Genomics 47:7‐11.
   Nelson, S.F., McCusker, J.H., Sander, M.A., Kee, Y., Modrich, P., and Brown, P.O. 1993. Genomic mismatch scanning: A new approach to genetic linkage mapping. Nature Genet. 4:11‐18.
   Perou, C.M., Jeffrey, S.S., van de Rijn, M., Rees, C.A., Eisen, M.B., Ross, D.T., Pergamenschikov, A., Williams, C.F., Zhu, S.X., Lee, J.C., Lashkari, D., Shalon, D., Brown, P.O., and Botstein, D. 1999. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc. Natl. Acad. Sci. U.S.A. 96:9212‐9217.
   Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.L., Chen, C., Zhai, Y., Dairkee, S.H., Ljung, B.M., Gray, J.W., and Albertson, D.G. 1988. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genet. 20:207‐211.
   Pollack, J.R., Perou, C.M., Alizadeh, A.A., Eisen, M.B., Pergamenschikov, A., Williams, C.F., Jeffrey, S.S., Botstein, D., and Brown, P.O. 1999. Genome‐wide analysis of DNA copy‐number changes using cDNA microarrays. Nature Genet. 23:41‐46.
   Solinas‐Toldo, S., Lampel, S., Stilgenbauer, S., Nickolenko, J., Benner, A., Dhner, H., Cremer, T., and Lichter, P. 1997. Matrix‐based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chrom. Cancer 20:399‐407.
   Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., and Futcher, B. 1998. Comprehensive identification of cell cycle–regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9:3273‐3297.
   Trent, J.M., Bittner, M., Zhang, J., Wiltshire, R., Ray, M., Su, Y., Gracia, E., Meltzer, P., De Risi, J., Penland, L., and Brown, P. 1997. Use of microgenomic technology for analysis of alterations in DNA copy number and gene expression in malignant melanoma. Clin. Exp. Immunol. 107:33‐40.
   Wilson, M., DeRisi, J., Kirstensen, H., Imboden, P., Rane, S., Brown, P., and Schoolnik, G. 1999. Exploring drug‐induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc. Natl. Acad. Sci. U.S.A. 96:12833‐12838.
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