Investigation Title Transcription profiling of Arabidopsis to investigate protective role of silicon in the Arabidopsis-powdery mildew pathosystem Comment[Submitted Name] The protective role of silicon in the Arabidopsis-powdery mildew pathosystem Experimental Design unknown_experiment_design_type transcription profiling by array Experimental Design Term Source REF EFO Comment[AEMIAMESCORE] 3 Comment[ArrayExpressReleaseDate] 2008-06-14 Comment[SecondaryAccession] GSE5718 Comment[ArrayExpressAccession] E-GEOD-5718 Comment[MAGETAB TimeStamp_Version] 2010-08-06 18:23:19 Last Changed Rev: 13058 Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Person Last Name Chain Person First Name Florian Person Mid Initials Person Email florian.chain.1@ulaval.ca Person Phone Person Fax Person Address Laval University, 2480, Hochelaga bd, Quebec, G1K 7P4, Canada Person Affiliation Laval University Person Roles submitter Person Roles Term Source REF Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2008-06-14 PubMed ID 17082308 Publication DOI 17082308 Publication Author List François Fauteux, Florian Chain, François Belzile, James G Menzies, Richard R Bélanger Publication Title The protective role of silicon in the Arabidopsis-powdery mildew pathosystem. Publication Status journal_article Publication Status Term Source REF The MGED Ontology Experiment Description The role and essentiality of silicon (Si) in plant biology has been debated for over 150 years in spite of numerous reports describing its beneficial properties. To obtain unique insights regarding the effect of Si on plants, we performed a complete transcriptome analysis of both control and powdery mildew-stressed Arabidopsis plants, with or without Si application, using a 44K microarray. Surprisingly, the expression of all but two genes was unaffected by Si in control plants, a result contradicting reports of possible direct effect of Si as a fertilizer. In contrast, inoculation of plants, treated or not with Si, altered the expression of a set of nearly 4,000 genes. Following functional categorization, many of the up-regulated genes were defense-related whereas a large proportion of down-regulated genes were involved in primary metabolism. Regulated defense genes included R genes, stress-related transcription factors, genes involved in signal transduction, the biosynthesis of stress hormones (SA, JA, ethylene), and the metabolism of reactive oxygen species. In inoculated plants treated with Si, the magnitude of down-regulation was attenuated by over 25%, an indication of stress alleviation. Our results demonstrate that Si treatment had no effect on the metabolism of unstressed plants suggesting a non essential role for the element, but that it has beneficial properties attributable to modulation of a more efficient response to pathogen stress. Experiment Overall Design: A loop design with complete dye-swap was used as experimental design for comparing plants submitted to four treatments and three biological replicates for a total of 24 Agilent Arabidopsis 3 microarrays. Two factors experimental factors : response to a compound (Silicon, treated or not treated) and disease state (Erysiphe cichoracearum, normal vs. diseased). Each factor had two levels. For each of the four combinations of factors, three plants were randomly selected. Thus a total of 12 plants were used for the experiment. RNA was extracted from rosette leaves. Protocol Name P-G5718-4 P-G5718-1 P-G5718-2 P-G5718-3 Protocol Type hybridization hybridization feature_extraction bioassay_data_transformation Protocol Description Hybridization was performed following Agilent's oligonucleotide microarray hybridization user's manual and Agilent's in situ Hybridization Plus kit. A volume of 200 ÂμL of combined Cy3- and Cy5-labeled cDNA targets were denatured at 98 °C for 3 min and cooled to room temperature. They were mixed with 50 ÂμL of 10x control targets, followed by the addition of 250 ÂμL of 2x hybridization buffer. The 500 ÂμL of reaction mix was applied to each Agilent 44K Arabidopsis 3 microarray (37,537 features), and hybridized in a hybridization rotation oven at 60 °C for 17 h. The slides were disassembled in 6 x SSC, 0.005% Triton X-102, washed first with 6xSSC, 0.005% Triton X-102 for 10 min at room temperature, then with 0.1 xSSC, 0.005% Triton X-102 for 5 min on ice, and dried using a nitrogen-filled air gun. The protocol and conditions used for hybridization, blocking and washing, including any post-processing steps such as staining: Hybridization was performed following Agilent's oligonucleotide microarray hybridization user's manual and Agilent's in situ Hybridization Plus kit. A volume of 200 µL of combined Cy3- and Cy5-labeled cDNA targets were denatured at 98 °C for 3 min and cooled to room temperature. They were mixed with 50 µL of 10x control targets, followed by the addition of 250 µL of 2x hybridization buffer. The 500 µL of reaction mix was applied to each Agilent 44K Arabidopsis 3 microarray (37,537 features), and hybridized in a hybridization rotation oven at 60 °C for 17 h. The slides were disassembled in 6 x SSC, 0.005% Triton X-102, washed first with 6xSSC, 0.005% Triton X-102 for 10 min at room temperature, then with 0.1 xSSC, 0.005% Triton X-102 for 5 min on ice, and dried using a nitrogen-filled air gun. The arrays were scanned using a dual-laser DNA microarray scanner (Agilent). The data was then extracted from images with Agilent’s Feature Extraction software 7.5. Data heading descriptions from GEO:
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#VALUE = Normalized Log Ratio (Loess followed by quantile) Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF The MGED Ontology SDRF File E-GEOD-5718.sdrf.txt Term Source Name NCBI Taxonomy The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/ http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version