Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize

J. M. Gardiner, C. R. Buell, R. Elumalai, David W Galbraith, D. A. Henderson, A. L. Iniguez, S. M. Kaeppler, J. J. Kim, J. Liu, A. Smith, L. Zheng, V. L. Chandler

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Analysis of gene expression on a genome scale can provide useful insights into plant growth and development, and an understanding of the mechanisms used by plants to cope with biotic and abiotic stress. To facilitate analysis of genome-wide gene expression in maize, we have assembled a large collection of maize EST and genomic sequences, designed a set of 57,442 maize 70-mer oligonucleotides to represent these sequences, and printed a two-slide microarray set (MOA and MOB) which is available to the maize research community at minimal cost. To monitor array quality, we have developed a series of printing controls and procedures that when coupled with a 9-mer hybridization assay, allow tracking of spot morphology and printing pin carryover. An optimized hybridization protocol has been developed by testing a series of hybridization temperatures and performing detailed statistical analyses. To facilitate management of all long-oligonucleotide associated array data, Zeamage, a Sybase relational database has been developed and is available at www.maizearray.org. Zeamage contains the appropriate tables and fields for tracking the oligonucleotide sequences and associated annotation, array design, and biological information associated with the microarray hybridizations. The www.maizearray.org web-site provides additional information on the project, array content, and data analysis tools.

Original languageEnglish (US)
Pages (from-to)425-435
Number of pages11
JournalMaydica
Volume50
Issue number3-4
StatePublished - 2005

Fingerprint

Microarray Analysis
oligonucleotides
Oligonucleotide Array Sequence Analysis
Zea mays
Printing
hybridization
corn
Oligonucleotides
Genome
Gene Expression
microarray technology
gene expression
Plant Development
genome
Expressed Sequence Tags
pins
biotic stress
Growth and Development
abiotic stress
plant development

Keywords

  • Gene expression
  • Maize
  • Microarrays
  • Oligonucleotides

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

Cite this

Gardiner, J. M., Buell, C. R., Elumalai, R., Galbraith, D. W., Henderson, D. A., Iniguez, A. L., ... Chandler, V. L. (2005). Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. Maydica, 50(3-4), 425-435.

Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. / Gardiner, J. M.; Buell, C. R.; Elumalai, R.; Galbraith, David W; Henderson, D. A.; Iniguez, A. L.; Kaeppler, S. M.; Kim, J. J.; Liu, J.; Smith, A.; Zheng, L.; Chandler, V. L.

In: Maydica, Vol. 50, No. 3-4, 2005, p. 425-435.

Research output: Contribution to journalArticle

Gardiner, JM, Buell, CR, Elumalai, R, Galbraith, DW, Henderson, DA, Iniguez, AL, Kaeppler, SM, Kim, JJ, Liu, J, Smith, A, Zheng, L & Chandler, VL 2005, 'Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize', Maydica, vol. 50, no. 3-4, pp. 425-435.
Gardiner JM, Buell CR, Elumalai R, Galbraith DW, Henderson DA, Iniguez AL et al. Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. Maydica. 2005;50(3-4):425-435.
Gardiner, J. M. ; Buell, C. R. ; Elumalai, R. ; Galbraith, David W ; Henderson, D. A. ; Iniguez, A. L. ; Kaeppler, S. M. ; Kim, J. J. ; Liu, J. ; Smith, A. ; Zheng, L. ; Chandler, V. L. / Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. In: Maydica. 2005 ; Vol. 50, No. 3-4. pp. 425-435.
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