Investigation Title Gene expression from Arabidopsis under high light conditions Comment[Submitted Name] Gene expression from Arabidopsis under high light conditions Experimental Design transcription profiling by array Experimental Design Term Source REF EFO Comment[SecondaryAccession] Comment[SecondaryAccession] GSE22671 Comment[ArrayExpressReleaseDate] 2010-07-29 Comment[AEMIAMESCORE] 4 Comment[ArrayExpressAccession] E-GEOD-22671 Comment[MAGETAB TimeStamp_Version] 2010-10-15 17:31:42 Last Changed Rev: 14677 Experimental Factor Name environmental stress Experimental Factor Type environmental stress Experimental Factor Term Source REF Person Last Name Dopazo Arellano GARCIA Revuelta Lorenzo Osuna Garcia-Garcia Gonzalez-Perez Person First Name Joaquin Juan FRANCISCO Jose Oscar Daniel Francisco Sergio Person Mid Initials B GARCIA L Person Email fgarcia@cipf.es Person Phone Person Fax Person Address Bionformatics and Genomics, CIPF, Av Autopista del Saler, 16, Valencia, Spain Person Affiliation CIPF Person Roles submitter Person Roles Term Source REF The MGED Ontology 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 2010-07-29 PubMed ID 21531897 Publication DOI 10.1104/pp.111.177766 Publication Author List González-Pérez S, Gutiérrez J, García-García F, Osuna D, Dopazo J, Lorenzo Ó, Revuelta JL, Arellano JB Publication Title Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions. Publication Status Publication Status Term Source REF Experiment Description We have investigated the genomic response of Arabidopsis cell suspension culture under high light. Our main goal has been twofold: first, to establish whether chloroplasts in Arabidopsis cell suspension culture are functional and, as such, can act as sensors of adverse external stimuli leading to the activation of genomic defence responses in a manner similar to that described in whole plants exposed to a wide range of environmental stresses and; second, to distinguish which of the ROS that would be probably generated in the chloroplasts is predominant. Our functional genomic analysis has led us to conclude that singlet oxygen is the major ROS in Arabidopsis cell suspension culture under high light stress and that singlet oxygen production is responsible for a genomic activation associated with the biosynthesis and signalling pathway of several phytohormones that ultimately triggers accelerated cell death. After the ninth day of growth, a volume of 200 mL of Arabidopsis cell suspension culture with a cell density of approximately 150-200 mg/mL was placed in a glass vessel surrounded by a water bath to maintain constant temperature during the light treatment. Nine microarray experiments were designed and classified as follows: control 1–3 (50 microE/m2/s), 1-h dark 1–3 and high light 1–3 (1800 microE/m2/s); where 1–3 stands for the number of biological replicates. After each treatment, sample RNA was extracted and its quality evaluated. The transcriptomic analysis was performed using Affymetrix GeneChip Arabidopsis genome ATH1 arrays. Protocol Name P-GSE22671-3 P-GSE22671-2 P-GSE22671-4 P-GSE22671-5 P-GSE22671-6 P-GSE22671-7 P-GSE22671-8 P-GSE22671-1 Protocol Type grow specified_biomaterial_action nucleic_acid_extraction labeling hybridization image_aquisition feature_extraction bioassay_data_transformation Protocol Description Arabidopsis cell suspension culture was maintained in 200 mL of liquid growth medium (Jouannea and Peaudlen, 1967; Axelos et al., 1992) by gentle agitation at 120 rpm at 24 ºC under continuous illumination (50 microE/m2/s) in an incubator shaker. Cells were sub-cultured with a 1/20 dilution factor every 7 days. An incubation of 30 min at high light or 1-h at dark were selected as the optimum time to monitor the changes in the transcription profile in the microarray experiments. Total RNA was extracted with the acid guanidine isothiocyanate-phenol-chloroform method using Trizol reagent. Total RNA was treated with TURBO DNase to eliminate traces of contaminating genomic DNA. Biotin-labelled cRNA was produced by in vitro transcription using GeneChip® 3' IVT Express Kit. The biotin-labelled cRNA was degraded by alkaline digestion and used for hybridization with ATH1 arrays. Technical steps as target hybridization, washing and staining of the arrays were performed sequentially as described in the Affymetrix GeneChip expression analysis technical manual using the Affymetrix once-cycle target labelling and control reagents, an Affymetrix GeneChip hybridization oven 640, and Affymetrix Fluidics Station 450 Microarrays were scanned using Affymetrix GenChip Scanner 3000 7G. Data was standardized from R using the affy Bioconductor package. Methods: Robust Multi-array Average and quantile normalization. ID_REF =
VALUE = RMA signal intensity Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology SDRF File E-GEOD-22671.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 Comment[AEExperimentType] transcription profiling by array