High-throughput, high-sensitivity analysis of gene expression in arabidopsis

Plant Physiology

Volumn 144, Issue 3, 2007, Pages 1256-1266

  Kris, Richard Martin ^a   Felder, Stephen ^a   Deyholos, Michael ^b,d   Lambert, Georgina M ^b   Hinton, James ^c   Botros, Ihab ^c   Martel, Ralph ^c   Seligmann, Bruce ^c   Galbraith, David W ^b  

^a LLC   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c High Throughput Genomics Inc ^*  (United States)

^d UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FORESTRY; GENE EXPRESSION; MICROARRAYS;

ARABIDOPSIS; NUCLEASE PROTECTION ASSAY; SALT STRESS;

PLANTS (BOTANY);

GENES; NUCLEIC ACIDS; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 34447131540     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.107.098681     Document Type: Article

References (26)

1. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, et al (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18: 630-634
2. Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK (2004) Realtime RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38: 366-379
3. Dafforn A, Chen P, Deng G, Herrler M, Iglehard D, Koritala S, Lato S, Pillarisetty S, Purohit R, Wang M, et al (2004) Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. Biotechniques 37: 854-857
4. Deyholos MK, Galbraith DW (2001) High-density DNA microarrays for gene expression analysis. Cytometry 43: 229-238
5. Fodor SPA, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251: 767-773
6. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537
7. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai HY, He YDD, et al (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126
8. Jenkins GI, Long JC, Wade HK, Shenton MR, Bibikova TN (2001) UV and blue light signalling: pathways regulating chalcone synthase gene expression in Arabidopsis. New Phytol 151: 121-131
9. Kim HS, Yu Y, Snesrud EC, Moy LP, Linford LD, Haas BJ, Nierman WC, Quackenbush J (2005) Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome. Plant J 41: 212-220
10. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, et al (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313: 1929-1935
11. Ma SS, Gong QQ, Bohnert HJ (2006) Dissecting salt stress pathways. J Exp Bot 57: 1097-1107
12. Martel RR, Botros IW, Rounseville MP, Hinton JP, Staples RR, Morales DA, Farmer JB, Seligmann BE (2002a) Multiplexed screening assay for mRNA combining nuclease protection with luminescent array detection. Assay Drug Dev Technol 1: 61-71
13. Martel RR, Rounesville MP, Botros IW, Kris R, Felder S, Seligmann BE (2002b) Multiplexed molecular profiling transcription assay in Array-Plates for high-throughput measurement of gene expression. In MP Weiner, Q Lu, eds, Gene Cloning and Expression Technologies. Easton Publishing, Westborough, MA, pp 549-564
14. Meyers BC, Galbraith DW, Nelson T, Agrawal V (2004) Methods for transcriptional profiling in plants: be fruitful and replicate. Plant Physiol 135: 637-652
15. Nakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2006) Transcriptional regulation of ABI3-and ABA-responsive genes including RD29B and RD29A in seeds, germinating embryos, and seedlings of Arabidopsis. Plant Mol Biol 60: 51-68
16. Nover L, Weigel D, Altmann T (2005) AtGenExpress project: arrays 3611-3622. http://web.uni-frankfurt.de/fb15/botanik/mcb/AFGN/atgenex.htm (December 29, 2006)
17. Nylander M, Svensson J, Palva ET, Welin BV (2001) Stress-induced accumulation and tissue-specific localization of dehydrins in Arabidopsis thaliana. Plant Mol Biol 45: 263-279
18. Raikhel N, Pirrung M (2005) Adding precision tools to the plant biologist's toolbox with chemical genomics. Plant Physiol 138: 563-564
19. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470
20. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506
21. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, et al (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31: 279-292
22. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F (1999) Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 17: 974-978
23. Sittampalam GS, Kahl SD, Janzen WP (1997) High throughput screening: advances in assay technologies. Curr Opin Chem Biol 1: 384-391
24. Strachan T, Abitbol M, Davidson D, Beckmann JS (1997) A new dimension for the human genome project: towards comprehensive expression maps. Nat Genet 16: 126-132
25. Takahashi S, Seki M, Ishida J, Satou M, Sakurai T, Narusaka M, Kamiya A, Nakajima M, Enju A, Akiyama K, et al (2004) Monitoring the expression profiles of genes induced by hyperosmotic, high salinity, and oxidative stress and abscisic acid treatment in Arabidopsis cell culture using a full-length cDNA microarray. Plant Mol Biol 56: 29-55
26. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270: 484-487