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Introduction to Microarray Technology

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DNA Microarrays for Biomedical Research

Part of the book series: Methods in Molecular Biology ((MIMB,volume 529))

Abstract

DNA microarrays can be used for large number of application where high-throughput is needed. The ability to probe a sample for hundred to million different molecules at once has made DNA microarray one of the fastest growing techniques since its introduction about 15 years ago. Microarray technology can be used for large scale genotyping, gene expression profiling, comparative genomic hybridization and resequencing among other applications. Microarray technology is a complex mixture of numerous technology and research fields such as mechanics, microfabrication, chemistry, DNA behaviour, microfluidics, enzymology, optics and bioinformatics. This chapter will give an introduction to each five basic steps in microarray technology that includes fabrication, target preparation, hybridization, detection and data analysis. Basic concepts and nomenclature used in the field of microarray technology and their relationships will also be explained.

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References

  1. 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.

    Article  PubMed  CAS  Google Scholar 

  2. Zammatteo, N., Jeanmart, L., Hamels, S., Courtois, S., Louette, P., Hevesi, L. and Remacle, J. (2000) Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal Biochem, 280, 143–150.

    Article  PubMed  CAS  Google Scholar 

  3. Ishkanian, A.S., Malloff, C.A., Watson, S.K., DeLeeuw, R.J., Chi, B., Coe, B.P., Snijders, A., Albertson, D.G., Pinkel, D., Marra, M.A. et al. (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet, 36, 299–303.

    Article  PubMed  CAS  Google Scholar 

  4. Lueking, A., Horn, M., Eickhoff, H., Bussow, K., Lehrach, H. and Walter, G. (1999) Protein microarrays for gene expression and antibody screening. Anal Biochem, 270, 103–111.

    Article  PubMed  CAS  Google Scholar 

  5. Huang, R.P. (2001) Detection of multiple proteins in an antibody-based protein microarray system. J Immunol Methods, 255, 1–13.

    Article  PubMed  CAS  Google Scholar 

  6. Huang, R.P., Huang, R., Fan, Y. and Lin, Y. (2001) Simultaneous detection of multiple cytokines from conditioned media and patient's sera by an antibody-based protein array system. Anal Biochem, 294, 55–62.

    Article  PubMed  CAS  Google Scholar 

  7. Li, Y., Lee, H.J. and Corn, R.M. (2006) Fabrication and characterization of RNA aptamer microarrays for the study of protein-aptamer interactions with SPR imaging. Nucleic Acids Res, 34, 6416–6424.

    Article  PubMed  CAS  Google Scholar 

  8. Lee, M. and Walt, D.R. (2000) A fiber-optic microarray biosensor using aptamers as receptors. Anal Biochem, 282, 142–146.

    Article  PubMed  CAS  Google Scholar 

  9. Bradner, J.E., McPherson, O.M., Mazitschek, R., Barnes-Seeman, D., Shen, J.P., Dhaliwal, J., Stevenson, K.E., Duffner, J.L., Park, S.B., Neuberg, D.S. et al. (2006) A robust small-molecule microarray platform for screening cell lysates. Chem Biol, 13, 493–504.

    Article  PubMed  CAS  Google Scholar 

  10. Wang, D., Liu, S., Trummer, B.J., Deng, C. and Wang, A. (2002) Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells. Nat Biotechnol, 20, 275–281.

    Article  PubMed  CAS  Google Scholar 

  11. Horlacher, T. and Seeberger, P.H. (2006) The utility of carbohydrate microarrays in glycomics. Omics, 10, 490–498.

    Article  PubMed  CAS  Google Scholar 

  12. Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995) Serial analysis of gene expression. Science, 270, 484–487.

    Article  PubMed  CAS  Google Scholar 

  13. Ekins, R., Chu, F. and Biggart, E. (1990) Fluorescence spectroscopy and its application to a new generation of high sensitivity, multi-microspot, multianalyte, immunoassay. Clin Chim Acta, 194, 91–114.

    Article  PubMed  CAS  Google Scholar 

  14. Ekins, R., Chu, F. and Biggart, E. (1990) Multispot, multianalyte, immunoassay. Ann Biol Clin (Paris), 48, 655–666.

    CAS  Google Scholar 

  15. Adey, N.B., Lei, M., Howard, M.T., Jensen, J.D., Mayo, D.A., Butel, D.L., Coffin, S.C., Moyer, T.C., Slade, D.E., Spute, M.K. et al. (2002) Gains in sensitivity with a device that mixes microarray hybridization solution in a 25-microm-thick chamber. Anal Chem, 74, 6413–6417.

    Article  PubMed  CAS  Google Scholar 

  16. MacBeath, G. and Schreiber, S.L. (2000) Printing proteins as microarrays for high-throughput function determination. Science, 289, 1760–1763.

    PubMed  CAS  Google Scholar 

  17. Kafatos, F.C., Jones, C.W. and Efstratiadis, A. (1979) Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Res, 7, 1541–1552.

    Article  PubMed  CAS  Google Scholar 

  18. 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.

    Article  PubMed  CAS  Google Scholar 

  19. Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C., Trent, J.M., Staudt, L.M., Hudson, J., Jr., Boguski, M.S. et al. (1999) The transcriptional program in the response of human fibroblasts to serum. Science, 283, 83–87.

    Article  PubMed  CAS  Google Scholar 

  20. 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. et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell, 2, 65–73.

    Article  PubMed  CAS  Google Scholar 

  21. 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.

    PubMed  CAS  Google Scholar 

  22. 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.

    Article  PubMed  CAS  Google Scholar 

  23. Galitski, T., Saldanha, A.J., Styles, C.A., Lander, E.S. and Fink, G.R. (1999) Ploidy regulation of gene expression. Science, 285, 251–254.

    Article  PubMed  CAS  Google Scholar 

  24. Perez-Diez, A., Morgun, A. and Shulzhenko, N. (2007) Microarrays for cancer diagnosis and classification. Advances in experimental medicine and biology, 593, 74–85.

    Article  PubMed  Google Scholar 

  25. Venier, P., De Pitta, C., Pallavicini, A., Marsano, F., Varotto, L., Romualdi, C., Dondero, F., Viarengo, A. and Lanfranchi, G. (2006) Development of mussel mRNA profiling: Can gene expression trends reveal coastal water pollution? Mutat Res.

    Google Scholar 

  26. Stangegaard, M., Wang, Z., Kutter, J.P., Dufva, M. and Wolff, A. (2006) Whole genome expression profiling using DNA microarray for determining biocompatibility of polymeric surfaces. Molecular Biosystems, 2, 421–428.

    Article  PubMed  CAS  Google Scholar 

  27. Stangegaard, M., Petronis, S., Jorgensen, A.M., Christensen, C.B. and Dufva, M. (2006) A biocompatible micro cell culture chamber (microCCC) for the culturing and on-line monitoring of eukaryote cells. Lab Chip, 6, 1045–1051.

    Article  PubMed  CAS  Google Scholar 

  28. Tusher, V.G., Tibshirani, R. and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A, 98, 5116–5121.

    Article  PubMed  CAS  Google Scholar 

  29. Frey, B.J., Mohammad, N., Morris, Q.D., Zhang, W., Robinson, M.D., Mnaimneh, S., Chang, R., Pan, Q., Sat, E., Rossant, J. et al. (2005) Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat Genet, 37, 991–996.

    Article  PubMed  CAS  Google Scholar 

  30. Castoldi, M., Schmidt, S., Benes, V., Noerholm, M., Kulozik, A.E., Hentze, M.W. and Muckenthaler, M.U. (2006) A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). Rna, 12, 913–920.

    Article  PubMed  CAS  Google Scholar 

  31. Beuvink, I., Kolb, F.A., Budach, W., Garnier, A., Lange, J., Natt, F., Dengler, U., Hall, J., Filipowicz, W. and Weiler, J. (2007) A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs. Nucleic Acids Res.

    Google Scholar 

  32. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P.O. and Davis, R.W. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A, 93, 10614–10619.

    Article  PubMed  CAS  Google Scholar 

  33. Loftus, S.K., Chen, Y., Gooden, G., Ryan, J.F., Birznieks, G., Hilliard, M., Baxevanis, A.D., Bittner, M., Meltzer, P., Trent, J. et al. (1999) Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis. Proc Natl Acad Sci U S A, 96, 9277–9280.

    Article  PubMed  CAS  Google Scholar 

  34. Matsuzaki, H., Dong, S., Loi, H., Di, X., Liu, G., Hubbell, E., Law, J., Berntsen, T., Chadha, M., Hui, H. et al. (2004) Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods, 1, 109–111.

    Article  PubMed  CAS  Google Scholar 

  35. Gunderson, K.L., Steemers, F.J., Lee, G., Mendoza, L.G. and Chee, M.S. (2005) A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet, 37, 549–554.

    Article  PubMed  CAS  Google Scholar 

  36. Chou, W.H., Yan, F.X., Robbins-Weilert, D.K., Ryder, T.B., Liu, W.W., Perbost, C., Fairchild, M., de Leon, J., Koch, W.H. and Wedlund, P.J. (2003) Comparison of two CYP2D6 genotyping methods and assessment of genotype-phenotype relationships. Clin Chem, 49, 542–551.

    Article  PubMed  CAS  Google Scholar 

  37. Gemignani, F., Perra, C., Landi, S., Canzian, F., Kurg, A., Tonisson, N., Galanello, R., Cao, A., Metspalu, A. and Romeo, G. (2002) Reliable detection of beta-thalassemia and G6PD mutations by a DNA microarray. Clin Chem, 48, 2051–2054.

    PubMed  CAS  Google Scholar 

  38. 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.

    Article  PubMed  CAS  Google Scholar 

  39. Fiegler, H., Redon, R., Andrews, D., Scott, C., Andrews, R., Carder, C., Clark, R., Dovey, O., Ellis, P., Feuk, L. et al. (2006) Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res, 16, 1566–1574.

    Article  PubMed  CAS  Google Scholar 

  40. 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. Nat Genet, 23, 41–46.

    Article  PubMed  CAS  Google Scholar 

  41. Barrett, M.T., Scheffer, A., Ben-Dor, A., Sampas, N., Lipson, D., Kincaid, R., Tsang, P., Curry, B., Baird, K., Meltzer, P.S. et al. (2004) Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A, 101, 17765–17770.

    Article  PubMed  CAS  Google Scholar 

  42. Pinkel, D. and Albertson, D.G. (2005) Array comparative genomic hybridization and its applications in cancer. Nat Genet, 37 Suppl, S11–17.

    Article  PubMed  Google Scholar 

  43. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., Fiegler, H., Shapero, M.H., Carson, A.R., Chen, W. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444–454.

    Article  PubMed  CAS  Google Scholar 

  44. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306–2309.

    Article  PubMed  CAS  Google Scholar 

  45. Malanoski, A.P., Lin, B., Wang, Z., Schnur, J.M. and Stenger, D.A. (2006) Automated identification of multiple micro-organisms from resequencing DNA microarrays. Nucleic Acids Res, 34, 5300–5311.

    Article  PubMed  CAS  Google Scholar 

  46. Lin, B., Wang, Z., Vora, G.J., Thornton, J.A., Schnur, J.M., Thach, D.C., Blaney, K.M., Ligler, A.G., Malanoski, A.P., Santiago, J. et al. (2006) Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res, 16, 527–535.

    Article  PubMed  CAS  Google Scholar 

  47. Lin, B., Blaney, K.M., Malanoski, A.P., Ligler, A.G., Schnur, J.M., Metzgar, D., Russell, K.L. and Stenger, D.A. (2007) Using a resequencing microarray as a multiple respiratory pathogen detection assay. J Clin Microbiol, 45, 443–452.

    Article  PubMed  CAS  Google Scholar 

  48. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., Winkler, J., Lockhart, D.J., Morris, M.S. and Fodor, S.P. (1996) Accessing genetic information with high-density DNA arrays. Science, 274, 610–614.

    Article  PubMed  CAS  Google Scholar 

  49. Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J. et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280, 1077–1082.

    Article  PubMed  CAS  Google Scholar 

  50. Ziauddin, J. and Sabatini, D.M. (2001) Microarrays of cells expressing defined cDNAs. Nature, 411, 107–110.

    Article  PubMed  CAS  Google Scholar 

  51. Palmer, E.L., Miller, A.D. and Freeman, T.C. (2006) Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis. BMC Genomics, 7, 145.

    Article  PubMed  Google Scholar 

  52. Ramachandran, N., Hainsworth, E., Bhullar, B., Eisenstein, S., Rosen, B., Lau, A.Y., Walter, J.C. and LaBaer, J. (2004) Self-assembling protein microarrays. Science, 305, 86–90.

    Article  PubMed  CAS  Google Scholar 

  53. Bruun, G.M., Wernersson, R., Juncker, A.S., Willenbrock, H. and Nielsen, H.B. (2007) Improving comparability between microarray probe signals by thermodynamic intensity correction. Nucleic Acids Res.

    Google Scholar 

  54. Dufva, M. (2005) Fabrication of high quality microarrays. Biomol Eng, 22, 173–184.

    Article  PubMed  CAS  Google Scholar 

  55. Moorcroft, M.J., Meuleman, W.R., Latham, S.G., Nicholls, T.J., Egeland, R.D. and Southern, E.M. (2005) In situ oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication. Nucleic Acids Res, 33, e75.

    Article  PubMed  Google Scholar 

  56. Southern, E.M., Case-Green, S.C., Elder, J.K., Johnson, M., Mir, K.U., Wang, L. and Williams, J.C. (1994) Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res, 22, 1368–1373.

    Article  PubMed  Google Scholar 

  57. 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.

    Article  PubMed  CAS  Google Scholar 

  58. Ohyama, H., Zhang, X., Kohno, Y., Alevizos, I., Posner, M., Wong, D.T. and Todd, R. (2000) Laser capture microdissection-generated target sample for high-density oligonucleotide array hybridization. Biotechniques, 29, 530–536.

    PubMed  CAS  Google Scholar 

  59. Gilbert, M.T., Haselkorn, T., Bunce, M., Sanchez, J.J., Lucas, S.B., Jewell, L.D., Van Marck, E. and Worobey, M. (2007) The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when? PLoS ONE, 2, e537.

    Article  PubMed  Google Scholar 

  60. Chomczynski, P. and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem, 162, 156–159.

    Article  PubMed  CAS  Google Scholar 

  61. Gilleland, R.C. and Hockett, R.D., Jr. (1998) Stability of RNA molecules stored in GITC. Biotechniques, 25, 944–946, 948.

    PubMed  CAS  Google Scholar 

  62. Van Gelder, R.N., von Zastrow, M.E., Yool, A., Dement, W.C., Barchas, J.D. and Eberwine, J.H. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A, 87, 1663–1667.

    Article  PubMed  Google Scholar 

  63. Eberwine, J., Yeh, H., Miyashiro, K., Cao, Y., Nair, S., Finnell, R., Zettel, M. and Coleman, P. (1992) Analysis of gene expression in single live neurons. Proc Natl Acad Sci U S A, 89, 3010–3014.

    Article  PubMed  CAS  Google Scholar 

  64. Kamme, F., Zhu, J., Luo, L., Yu, J., Tran, D.T., Meurers, B., Bittner, A., Westlund, K., Carlton, S. and Wan, J. (2004) Single-cell laser-capture microdissection and RNA amplification. Methods Mol Med, 99, 215–223.

    PubMed  CAS  Google Scholar 

  65. 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. et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol, 19, 342–347.

    Article  PubMed  CAS  Google Scholar 

  66. Gupta, V., Cherkassky, A., Chatis, P., Joseph, R., Johnson, A.L., Broadbent, J., Erickson, T. and DiMeo, J. (2003) Directly labeled mRNA produces highly precise and unbiased differential gene expression data. Nucleic Acids Res, 31, e13.

    Article  PubMed  Google Scholar 

  67. Stangegaard, M., Dufva, I.H. and Dufva, M. (2006) Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA. Biotechniques, 40, 649–657.

    Article  PubMed  CAS  Google Scholar 

  68. Huber, M., Wei, T.F., Muller, U.R., Lefebvre, P.A., Marla, S.S. and Bao, Y.P. (2004) Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA. Nucleic Acids Res, 32, e137.

    Article  PubMed  Google Scholar 

  69. Liu, R., Lenigk, R., Druyor-Sanchez, R., Yang, J. and Grodzinski, P. (2003) Hybridization enhancement using cavitation microstreaming. Anal Chem, 75, 1911–1917.

    Article  PubMed  CAS  Google Scholar 

  70. Yuen, P., Li, G., Bao, Y. and Muller, U. (2003) Microfluidic devices for fluidic circulation and mixing improve hybridization signal intensity on DNA arrays. Lab on a Chip, 3, 46–50.

    Article  PubMed  CAS  Google Scholar 

  71. Bynum, M.A. and Gordon, G.B. (2004) Hybridization enhancement using microfluidic planetary centrifugal mixing. Anal Chem, 76, 7039–7044.

    Article  PubMed  CAS  Google Scholar 

  72. Pappaert, K., Vanderhoeven, J., Van Hummelen, P., Dutta, B., Clicq, D., Baron, G.V. and Desmet, G. (2003) Enhancement of DNA micro-array analysis using a shear-driven micro-channel flow system. J Chromatogr A, 1014, 1–9.

    Article  PubMed  CAS  Google Scholar 

  73. Hessner, M.J., Wang, X., Khan, S., Meyer, L., Schlicht, M., Tackes, J., Datta, M.W., Jacob, H.J. and Ghosh, S. (2003) Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. Nucleic Acids Res, 31, e60.

    Article  PubMed  Google Scholar 

  74. Hessner, M.J., Wang, X., Hulse, K., Meyer, L., Wu, Y., Nye, S., Guo, S.W. and Ghosh, S. (2003) Three color cDNA microarrays: quantitative assessment through the use of fluorescein-labeled probes. Nucleic Acids Res, 31, e14.

    Article  PubMed  Google Scholar 

  75. Lindroos, K., Sigurdsson, S., Johansson, K., Ronnblom, L. and Syvanen, A.C. (2002) Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res, 30, e70.

    Article  PubMed  Google Scholar 

  76. Bao, Y.P., Huber, M., Wei, T.F., Marla, S.S., Storhoff, J.J. and Muller, U.R. (2005) SNP identification in unamplified human genomic DNA with gold nanoparticle probes. Nucleic Acids Res, 33, e15.

    Article  PubMed  Google Scholar 

  77. Hesse, J., Jacak, J., Kasper, M., Regl, G., Eichberger, T., Winklmayr, M., Aberger, F., Sonnleitner, M., Schlapak, R., Howorka, S. et al. (2006) RNA expression profiling at the single molecule level. Genome Res, 16, 1041–1045.

    Article  PubMed  CAS  Google Scholar 

  78. Han, A., Dufva, M., Belleville, E. and Christensen, C. (2003) Detection of analyte binding to microarrays using gold nano particles labels and a desktop scanner. Lab Chip, 3, 336–339.

    Google Scholar 

  79. Alexandre, I., Hamels, S., Dufour, S., Collet, J., Zammatteo, N., De Longueville, F., Gala, J.L. and Remacle, J. (2001) Colorimetric silver detection of DNA microarrays. Anal Biochem, 295, 1–8.

    Article  PubMed  CAS  Google Scholar 

  80. Petersen, J., Stangegaard, M., Birgens, H. and Dufva, M. (2007) Detection of mutations in the beta-globin gene by colorimetric staining of DNA microarrays visualized by a flatbed scanner. Anal Biochem, 360, 169–171.

    Article  PubMed  CAS  Google Scholar 

  81. Chen, J.J., Wu, R., Yang, P.C., Huang, J.Y., Sher, Y.P., Han, M.H., Kao, W.C., Lee, P.J., Chiu, T.F., Chang, F. et al. (1998) Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection. Genomics, 51, 313–324.

    Article  PubMed  CAS  Google Scholar 

  82. Eisen, M.B. and Brown, P.O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol, 303, 179–205.

    Article  PubMed  CAS  Google Scholar 

  83. Workman, C., Jensen, L.J., Jarmer, H., Berka, R., Gautier, L., Nielser, H.B., Saxild, H.H., Nielsen, C., Brunak, S. and Knudsen, S. (2002) A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol, 3, research0048.

    Google Scholar 

  84. Luebke, K.J., Balog, R.P. and Garner, H.R. (2003) Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts. Nucleic Acids Res, 31, 750–758.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

Thanks are due to David Sabourin, Lena Poulsen and Jesper Petersen for reading the manuscript and helpful discussions.

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Dufva, M. (2009). Introduction to Microarray Technology. In: Dufva, M. (eds) DNA Microarrays for Biomedical Research. Methods in Molecular Biology, vol 529. Humana Press. https://doi.org/10.1007/978-1-59745-538-1_1

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