Investigation Title Transcription profiling of Arabidopsis response to Erysiphe orontii infection - AtGenExpress Comment[Submitted Name] AtGenExpress: Pathogen Series: Response to Erysiphe orontii infection Experimental Design time series design Experimental Design Term Source REF Comment[AEExperimentType] transcription profiling by array Comment[AEExperimentDisplayName] Transcription profiling by array of Arabidopsis after inoculation with Erysiphe orontii Comment[ArrayExpressReleaseDate] 2008-06-14 Comment[SecondaryAccession] GSE5686 Comment[AEMIAMESCORE] 4 Comment[ArrayExpressAccession] E-GEOD-5686 Comment[MAGETAB TimeStamp_Version] 2010-08-06 18:14:50 Last Changed Rev: 13058 Experimental Factor Name inoculation treatment time Experimental Factor Type infect time Experimental Factor Term Source REF Person Last Name (NASC) Person First Name Nottingham Arabidopsis Stock Centre Person Mid Initials Person Email affy@arabidopsis.info Person Phone Person Fax Person Address School of Biosciences, University of Nottingham, Nottingham Arabidopsis Stock Centre (NASC), Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom Person Affiliation Nottingham Arabidopsis Stock Centre (NASC) 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 Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana; The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Responses to E. orontii infection were assayed in wild-type Col-0 plants at 6, 12, 18, 24, 48, 72, 96, and 120 hours after inoculation of adult leaves. Inoculation was done via settling tower, using 10 day old E. orontii cultures. Leaves number 7 to 10 were selected for profiling. Experimenter name = Fred Ausubel , Julia Dewdney; Experimenter institute = AtGenExpress Experiment Overall Design: 48 samples were used in this experiment Protocol Name P-G5686-6 P-G5686-13 P-G5686-11 P-G5686-3 P-G5686-7 P-G5686-16 P-G5686-2 P-G5686-4 P-G5686-15 P-G5686-1 P-G5686-10 P-G5686-9 P-G5686-14 P-G5686-12 P-G5686-8 P-G5686-5 Affymetrix:Protocol:Hybridization-Unknown P-AFFY-6 Protocol Type specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action hybridization feature_extraction Protocol Description Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 4 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 18 hours post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 12 hours post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 3 days post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 5 days post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 24 hours post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 2 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 3 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 24 hours post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 2 days post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 6 hours post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 6 hours post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 18 hours post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 12 hours post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 5 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 4 days post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period. Title: Affymetrix Generic Hybridization. Description: Title: Affymetrix CEL analysis. Description: Protocol Parameters Protocol Hardware Protocol Software MicroArraySuite 5.0 MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF SDRF File E-GEOD-5686.sdrf.txt Term Source Name EFO Term Source File http://www.ebi.ac.uk/efo/ Term Source Version