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Arabidopsis Oligonucleotide Microarrays


 

We are printing 29,000 element Arabidopsis Oligonucleotide Microarrays, using the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0.  Arrays cost $115 each, and are available to university, government, and not-for profit scientists.  Further details of the Oligo set, including the 70-mer sequence information, can be found at the Operon website (http://omad.operon.com/download/index.php).

Prior to September 2004, we were printing the Operon Arabidopsis Genome Oligo Set Version 1.0. This set comprised 26,000 oligonucleotides.  Operon has now discontinued its production. For archival files providing information for locating genes on these arrays, please follow this link.

We are also printing: (1) 45,000 element Rice Oligonucleotide Microarrays.  For more information, follow this link. (2) 16,000 element Medicago Oligonucleotide Microarrays. Please follow this link for background information.  If you are interested in obtaining Medicago microarrays, please contact David Galbraith.

We are offering hybridization services for Agilent long oligomer microarrays.  Agilent expects to provide whole genome arrays for up to 30 agbio species, including pig, sheep, Arabidopsis, rabbit, tomato, soybean, Brassica, tobacco, cotton, and wheat. For more information please contact David Galbraith.

We are also offering full cell type-specific expression profiling services, based on our recent publications (see reference 23, below).  For further information, please follow this link.

 

 

*Please note the microarrays are shipped prior to UV cross-linking.  Cross-linking MUST BE DONE according to the protocol provided here before hybridization.

Microarray production, results, and protocol information provided by Dr. R. Elumalai, Dr. F.C. Gong, Dr. R. Formosa, Ms. M. Gchachu, Dr. H. Ozkan, Mr. T. Watson, Ms. L. Cheam, and Dr. J. Janda.



Recent publications using these microarrays

 

  1. Boyce JM, Knight H, Deyholos M, Openshaw M, Galbraith DW, Warren G, Knight MR (2003). The sfr6 mutant of Arabidopsis is defective in transcriptional activation via CBF/DREB1 and DREB2 and shows sensitivity to osmotic stress.  Plant Journal 34:395-406.
  2. Armengaud P, Breitling R, Amtmann A (2004). The potassium-dependent transcriptome of Arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling. Plant Physiology 136:2556-2576.
  3. Miyazaki S, Fredricksen M, Hollis KC, Poroyko V, Shepley D, Galbraith DW, Long SP, Bohnert HJ (2004). Transcript expression profiles of Arabidopsis thaliana grown under controlled conditions and open-air elevated concentrations of CO2 and of O3. Field Crops Research 90:47-59.
  4. Downie AL, Miyazaki S, Bohnert HJ, John P, Coleman JOD, Parry MAJ, Haslam RP (2004). Methanol-regulated gene expression in Arabidopsis thaliana. Phytochemistry 65:2305-2316.
  5. Ma S, Quist T, Ulanov A, Quigley F, Joly R, Bohnert HJ (2004). Suppression of γ-TIP in Arabidopsis leads to cell and plant death. Plant Journal 40:845-859.
  6. Kristensen C, Morant M, Olsen CE, Galbraith DW, Lindberg-Mřller B, Bak S (2005). Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome.  Proc. Natl. Acad. Sci. U.S.A. 102:1779-1884.
  7. Gong Q, Li P, Ma S, Rupassara SI, Bohnert HJ (2005).  Stress adaptation competence in Arabidopsis thaliana and its extremophile relative Thellungiella halophila. Plant Journal 44:826-839.
  8. Pylatuik JD, Fobert PR (2005). Comparison of transcript profiling on Arabidopsis microarray platform technologies. Plant Molecular Biology 58:609-624.
  9. Campanella, J. Vega, Q. Du, C., Graff, W. Gomes, O.  (2005) A microarray analysis of gene regulation in radiation-induced plant tumor and Arabidopsis thaliana tissues.  In Vivo 27:9-19.
  10. Sioson AS, Mane SP, Li P, Sha W, Heath LS, Bohnert HJ, Grene R (2006). The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison. B.M.C. Bioinformatics 2006, 7:215 doi:10.1186/1471-2105-7-215.
  11. Li P, Mane SP, Sioson AA, Heath LS, Bohnert HJ, Grene R (2006). Effects of chronic ozone exposure on gene expression in Arabidopsis thaliana ecotypes and in Thellungiella halophila. Plant Cell Environment 29:854-868.
  12. Ma S, Gong Q, Bohnert HJ (2006). Dissecting salt stress pathways. Journal of Experimental Botany 57:1097-1107.
  13. Rangwala SH, Elumalai R, Vanier C, Ozkan H, Galbraith DW, Richards EJ (2006). Meiotically-stable natural epigenetic variation in Sadhu, a novel Arabidopsis retroposon. P.L.O.S. Genetics 2:270-281.
  14. Mahalingam R, Jambunathan N, Gunjan SK, Faustin E, Weng H, Ayoubi P (2006). Analysis of oxidative signaling induced by ozone in Arabidopsis thaliana. Plant Cell and Environment 29:1357-1371.
  15. Rius S, Casati P, Iglesias A,  Gomez-Casati DF (2006). Characterization of an Arabidopsis thaliana mutant lacking a cytosolic non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase. Plant Molecular Biology 61:945-957.
  16. Maathuis FJM (2006) cGMP modulates gene transcription and cation transport in Arabidopsis roots. Plant Journal 45:700-711.
  17. Moscatiello R, Mariani P, Sanders D, Maathuis FJM (2006). Transcriptional analysis of calcium-dependent and calcium-independent signaling pathways induced by oligogalacturonides. Journal of Experimental Botany 57:2847-2865.
  18. Keurentjes JJB, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G, Snoek LB, Peeters AJM, Vreugdenhil D, Koornneef M, Jansen RC (2007). Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc. Natl. Acad. Sci. U.S.A. 104:1708-1713.
  19. Adie BAT, Pérez-Pérez J, Pérez-Pérez MM, Godoy M, Sánchez-Serrano J-J, Schmelz EA, Solano R (2007). ABA is an essential signal for plant resistance to pathogens affecting JA biosynthesis and the activation of defenses in Arabidopsis. Plant Cell 19:1665-1681.
  20. Broekgaarden C, Poelman EH, Steenhuis G, Voorrips RE, Dicke M, Vosman B (2007). Genotypic variation in genome-wide transcription profiles induced by insect feeding: Brassica oleracea – Pieris rapae interactions. B.M.C. Genomics 8:239 doi:10.1186/1471-2164-8-239.
  21. Chini A, Fonseca S, Fernández G, Adie B, Chico JM, Lorenzo O, García-Casado G, López-Vidriero I, Lozano FM, Ponce MR, Micol JL, Solano R (2007). The JAZ family of repressors is the missing link in jasmonate signaling. Nature 448:666-671.
  22. Bueso E, Alejandro S, Carbonell P, Perez-Amador MA, Fayos F, Bellés JM, Rodriguez PL, Serrano R (2007). The lithium tolerance of the Arabidopsis cat2 mutant reveals a cross-talk between oxidative stress and ethylene. Plant Journal 52:1052-1065.
  23. Zhang H, Kim M-S, Krishnamachari V, Payton P, Sun Y, Grimson M, Farag MA, Ryu C-M, Allen R, Melo IS, Paré PW (2007). Rhizobacterial volatile emissions regulate auxin homeostasis and cell expansion in Arabidopsis. Planta 226:839-851.
  24. Zhang CQ, Lambert GM, Barthelson RA, Galbraith DW (2008). Characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiology 147:30-40. 
  25. Weston DJ, Gunter LE, Rogers A, Wullschleger SD (2008). Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants. BMC Systems Biology 2: Article Number 16.
  26. Zhang H, Kim MS, Sun Y, Dowd SE, Shi HZ, Paré PW (2008). Soil bacteria confer plant salt tolerance by tissue-specific regulation of the sodium transporter HKT1. Molecular Plant-Microbe Interactions 21:737-744.
  27. Zhang H, Xie X, Kim M-S, Kornyeyev DA, Holaday S, Paré PW (2008). Soil bacteria augment Arabidopsis photosynthesis by decreasing glucose sensing and abscisic acid levels in planta. Plant Journal 56:264-273.
  28. Agudelo-Romero P, Carbonell P, Perez-Amador MA, Elena SF (2008). Virus adaptation by manipulation of host’s gene expression. PLoS ONE 3:e2397.
  29. Agudelo-Romero P, Carbonell P, de la Iglesia F. Carrera J, Rodrigo G, Jaramillo A, Perez-Amador MA, Elena SF (2008). Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco Etch Virus. Virology Journal 5:92.
  30. Broekgaarden C, Poelman EH, Steenhuis G, Voorrips RE, Dicke M, Vosman B (2008). Responses of Brassica oleracea cultivars to infestation by the aphid Brevicoryne brassicae: an ecological and molecular approach. Plant Cell and Environment 31:1592-1605.
  31. Fatouros NE, Broekgaarden C, Bukovinszkiné Kiss G, Van Loon JJA, Mumm R, Huigens ME, Dicke M, Hilker M (2008). Male-derived butterfly anti-aphrodisiac mediates induced indirect plant defense. Proceedings of the National Academy of Sciences USA 105:10033-10038.
  32. Rius S, Casati P, Iglesias A, Gomez-Casati DF (2008). Characterization of Arabidopsis thaliana lines deficient in GAPC-1, a cytosolic NAD-dependent glyceraldehyde 3-phosphate dehydrogenase. Plant Physiology 148:1655-1667.

 

Purchase of instruments used for microarray production and analysis was made possible in part by funding from the National Science Foundation.

Questions or comments should be addressed to: David Galbraith
Page last updated February 15, 2010