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Transcription profiling of Arabidopsis leaf samples treated with salicylic acid

ABSTRACT: Arabidopsis plants, ecotype Columbia, were sprayed with surfactant alone (0.01% Silwet) or surfactant and 1mM salicylic acid until all leaves were wet, 3 to 4 weeks after germination (before flowering). Leaves were harvested and frozen in liquid nitrogen. Three biological replicates were obtained over a period of 6 months. For each replicate, RNA was extracted using standard phenol/chloroform protocol and biotin-labeled cRNA was synthesized. cRNA was hybridized to 6 ATH1 GeneChip arrays. Cel files produced by the Affymetrix software were imported into R. Background subtraction, normalization and probe summaries were performed with the rma, quantile.normalization and median polish options of the rma function. Comparison of the SA- versus mock-treated tissue provides insight on the genes involved in systemic acquired resistance in Arabidopsis. Experiment Overall Design: 3 mock-treated and 3 SA-treated biological replicates were analyzed (one array each)

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Francoise Thibaud-Nissen 

PROVIDER: E-GEOD-3984 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants.

Thibaud-Nissen Françoise F   Wu Hank H   Richmond Todd T   Redman Julia C JC   Johnson Christopher C   Green Roland R   Arias Jonathan J   Town Christopher D CD  

The Plant journal : for cell and molecular biology 20060701 1

We have developed two long-oligonucleotide microarrays for the analysis of genome features in Arabidopsis thaliana, in particular for the high-throughput identification of transcription factor-binding sites. The first platform contains 190,000 probes representing the 2-kb regions upstream of all annotated genes at a density of seven probes per promoter. The second platform is divided into three chips, each of over 390,000 features, and represents the entire Arabidopsis genome at a density of one  ...[more]

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