Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species

Plant Biotechnology Journal

Volumn 2, Issue 1, 2004, Pages 45-57

  Lee, Hyeon Se ^a   Wang, Jianlin ^a   Tian, Lu ^a   Jiang, Hongmei ^b,c   Black, Michael A ^b,c,f   Madlung, Andreas ^d,g   Watson, Brian ^d   Lukens, Lewis ^e,h   Pires, J Chris ^e   Wang, Jiyuan J ^a   Comai, Luca ^d   Osborn, Thomas C ^e   Doerge, R W ^b,c   Chen, Z Jeffrey ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

^c PURDUE UNIVERSITY   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

^e UNIVERSITY OF WISCONSIN MADISON   (United States)

^f UNIVERSITY OF AUCKLAND   (New Zealand)

^g UNIVERSITY OF PUGET SOUND   (United States)

^h UNIVERSITY OF GUELPH   (Canada)

Author keywords

70 mer oligo; Analysis of variance (ANOVA); Arabidopsis; Brassica; Dye swap; Microarray

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS ARENOSA; ARABIDOPSIS THALIANA; BRASSICA; BRASSICA OLERACEA; BRASSICA OLERACEA VAR. CAPITATA; CAENORHABDITIS; CAENORHABDITIS ELEGANS; EMBRYOPHYTA; EUKARYOTA;

EID: 3042529193     PISSN: 14677644     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1467-7652.2003.00048.x     Document Type: Article

References (45)

1. Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
2. Bachem., C.W., van der Hoeven, R.S., de Bruijn, S.M., Vreugdenhil, D., Zabeau, M. and Visser, R.G. (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J. 9, 745-753.
3. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soci (Series B), 57, 289-300.
4. Black, M.A. (2002) Statistical issues in the design and analysis of spotted microarray experiments. PhD Thesis, West Lafayette, Indiana: Department of Statistics, Purdue University.
5. Black, M.A. and Doerge, R.W. (2002) Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiment. Bioinformatics, 18, 1609-1616.
6. Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., Roth, R., George, D., Eletr, S., Albrecht, G., Vermaas, E., Williams, S.R., Moon, K., Burcham, T., Pallas, M., DuBridge, R.B., Kirchner, J., Fearon, K., Mao, J. and Corcoran, K. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630-634.
7. Cavell, A.C., Lydiate, D.J., Parkin, I.A., Dean, C. and Trick, M. (1998) Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome, 41, 62-69.
8. Chen, Z.J., Comai, L. and Pikaard, C.S. (1998) Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc Natl Acad. Sci. USA, 95, 14891-14896.
9. 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, 680-685.
10. Dudley, A.M., Aach, J., Steffen, M.A. and Church, G.M. (2002) Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl Acad. Sci. USA, 99, 7554-7559.
11. Eisen, M.B. and Brown, P.O. (1999) DNA arrays for analysis of gene expression. Meth. Enzymol. 303, 179-205.
12. Finkelstein, D., Ewing, R., Gollub, J., Sterky, F., Cherry, J.M. and Somerville, S. (2002) Microarray data quality analysis: lessions from the AFGC project. Plant Mol. Biol. 48, 119-131.
13. 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.
14. Girke, T., Todd, J., Ruuska, S., White, J., Benning, C. and Ohlrogge, J. (2000) Microarray analysis of developing Arabidopsis seeds. Plant Physiol. 124, 1570-1581.
15. Hall, A.E., Fiebig, A. and Preuss, D. (2002) Beyond the Arabidopsis genome: Opportunities for comparative genomics. Plant Physiol. 129, 1439-1447.
16. Hanfstingl, U., Berry, A., Kellogg, E.A., Costa, J.T., 3rd, Rudiger, W. and Ausubel, F.M. (1994) Haplotypic divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: Roles for both balancing and directional selection? Genetics, 138, 811-828.
17. Hartl, D.L., Meiklejohn, C.D., Castillo-Davis, C.I., Cavalieri, D., Ranz, J.M. and Townsend, J.P. (2003) Gene expression profiling in evolutionary genetics. In: The Evolution of Population Biology: Modern Synthesis (Singh, R., Jain, S. and Uyenoyama, M., eds), pp. 74-93. New York: Academic Press.
18. Henikoff, S. and Comai, L. (1998) A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics, 149, 307-318.
19. Hochberg, Y. and Tamhane, A.C. (1987) Multiple Comparison Procedures. New York: Wiley.
20. Horvath, D.P., Schaffer, R., West, M. and Wisman, E. (2003) Arabidopsis microarrays identify conserved and differentially expressed genes involved in shoot growth and development from distantly related plant species. Plant J. 34, 125-134.
21. 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, 342-347.
22. Kerr, M.K. and Churchill, G.A. (2001) Experimental design for gene expression microarrays. Biostatistics, 2, 183-201.
23. Knight, J. (2001) When the chips are down. Nature, 410, 860-861.
24. Koch, M.A., Haubold, B. and Mitchell-Olds, T. (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol, 17, 1483-1498.
25. Koch, M., Haubold, B. and Mitchell-Olds, T. (2001) Molecular systematics of the Brassicaceae: Evidence from coding plastidic matK and nuclear Chs sequences. Am. J. Bot. 88, 534-544.
26. Lee, H.S. and Chen, Z.J. (2001) Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl Acad. Sci. USA, 98, 6753-6758.
27. Li, F. and Stormo, G.D. (2001) Selection of optimal DNA oligos for gene expression arrays. Bioinformatics, 17, 1067-1076.
28. Lukens, L., Zou, F., Lydiate, D., Parkin, I. and Osborn, T. (2003) Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana. Genetics, in press.
29. Madlung, A., Masuelli, R.W., Watson, B., Reynolds, S.H., Davison, J. and Comai, L. (2002) Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 129, 733-746.
30. Mitchell-Olds, T. and Clauss, M.J. (2002) Plant evolutionary genomics. Curr. Opin. Plant Biol. 5, 74-79.
31. Nilsen, T.W., Grayzel, J. and Prensky, W. (1997) Dendritic nucleic acid structures. J. Theor. Biol. 187, 273-284.
32. Randolph, J.B. and Waggoner, A.S. (1997) Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes. Nucl. Acids Res. 25, 2923-2929.
33. Relogio, A., Schwager, C., Richter, A., Ansorge, W. and Valcarcel, J. (2002) Optimization of oligonucleotide-based DNA microarrays. Nucl. Acids Res. 30, e51.
34. Rifkin, S.A., Kim, J. and White, K.P. (2003) Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet, 33, 138-144.
35. Sanger, F., Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5467.
36. Schena, M., Heller, R.A., Theriault, T.P., Konrad, K., Lachenmeier, E. and Davis, R.W. (1998) Microarrays: Biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16, 301-306.
37. 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.
38. Singh-Gasson, S., Green, R.D., Yue, Y., Nelson, C., Blattner, F., Sussman, M.R. and Cerrina, F. (1999) Maskless fabrication of light-directed oligonucleotide microarrays using a digital micro-mirror array. Nat. Biotechnol. 17, 974-978.
39. Stears, R.L., Getts, R.C. and Gullans, S.R. (2000) A novel, sensitive detection system for high-density microarrays using dendrimer technology. Physiol. Genomics, 3, 93-99.
40. Townsend, J.P., Cavalieri, D. and Hartl, D.L. (2003) Population genetic variation in genome-wide gene expression. Mol. Biol. Evol, 20, 955-963.
41. Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
42. Velculescu, V.E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett, D.E. Jr, Hieter, P., Vogelstein, B. and Kinzler, K.W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
43. Wang, H.-W., Malek, R.L., Kwitek, A.E., Greene, A.S., Luu, T.V., Behbahani, B., Frank, B., Quackenbush, J. and Lee, N.H. (2003) Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol. 4, R5.1-R5.13.
44. Wang, Y., Wang, X., Guo, S.W. and Ghosh, S. (2002) Conditions to ensure competitive hybridization in two-color microarray: a theoretical and experimental analysis. Biotechniques, 32, 1342-1346.
45. Yuen, T., Wurmbach, E., Pfeffer, R.L., Ebersole, B.J. and Sealfon, S.C. (2002) Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucl. Acids Res. 30, e48.