Investigation Title Expression data from Arabidopsis gapcp mutant treated with ABA Comment[Submitted Name] Expression data from Arabidopsis gapcp mutant treated with ABA Experimental Design genetic modification design Experimental Design Term Source REF EFO Comment[AEExperimentType] transcription profiling by array Comment[AEExperimentDisplayName] Transcription profiling by array of Arabidopsis gapcp mutants treated with abscisic acid. Comment[SecondaryAccession] Comment[SecondaryAccession] GSE21765 Comment[ArrayExpressReleaseDate] 2010-05-28 Comment[AEMIAMESCORE] 4 Comment[ArrayExpressAccession] E-GEOD-21765 Comment[MAGETAB TimeStamp_Version] 2010-08-04 06:52:02 Last Changed Rev: 13058 Experimental Factor Name genotype Experimental Factor Type genotype Experimental Factor Term Source REF Person Last Name Ros Person First Name Roc Person Mid Initials Person Email roc.ros@uv.es Person Phone Person Fax Person Address Biologia Vegetal, Universitat de Valencia, Vicent Andres Estelles, Burjassot, 46100, spain Person Affiliation Universitat de Valencia 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 2010-05-28 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2). gapcp double mutants (gapcp1 gapcp2) display a drastic phenotype of arrested root development and sterility.Complex interactions occurring between ABA and sugar signal transduction pathways have been shown, but the molecular mechanisms connecting both pathways are not well understood. Since we found drastic carbohydrate changes in gapcp1 gapcp2, we studied their response to ABA. by performing a microarray analysis comparing gapcp1 gapcp2 and wild type seedlings after a long term treatment with ABA. 15-day old Arabidopsis seedlings (Col 0) and gapcp1gapcp2 double mutants were used for RNA extraction and hybridization on Affymetrix microarrays. Protocol Name P-GSE21765-3 P-GSE21765-4 P-GSE21765-2 P-GSE21765-5 P-GSE21765-6 P-GSE21765-7 P-GSE21765-8 P-GSE21765-1 Protocol Type grow nucleic_acid_extraction specified_biomaterial_action labeling hybridization image_aquisition feature_extraction bioassay_data_transformation Protocol Description Seeds were germinated and grown vertically in MS 1/5 with Gamborg vitamins. Light condicitions: 16 hours light, 8 hours dark. Temperature: 22ºC. Light 100 μmol m−2 s−1. Total RNA was extracted using the RNeasy plant mini kit (Qiagen).RNA was extracted from three sets of gapcp double mutants and wild type plants grown at the same time. RNA integrity was determined using RNA 6000 Nano Labchips® in an Agilent 2100 Bioanalyzer following the manufactures protocol. The purified RNA (8 μg) was used to generate first-strand cDNA in a reverse transcription reaction (One-Cycle Target Labeling and Control Reagents; Affymetrix). After second-strand synthesis, the double-stranded cDNAs were used to generate cRNA via an in vitro transcriptional reaction. Seedlings were treated with 0,75 microM ABA for 8 days The cRNA was labeled with biotin, and 20 μg of the labeled cRNA was fragmented. The size distribution of the cRNAs and fragmented cRNAs was assessed using an Eppendorf Biophotometer and electrophoresis. Fragmented cRNA (15 μg) was added to 300 μL of hybridization solution, and 200 μL of this mixture was used for hybridization on Arabidopsis ATH1 Genome Arrays for 16 h at 45°C. The standard wash and double-stain protocols (EukGE-WS2v5-450) were applied using an Affymetrix GeneChip Fluidics Station 450. The arrays (three replicates of each treatment) were scanned on an Affymetrix GeneChip scanner 3000. Fluorescence images were normalized with the software GCOS from Affymetrix. Data were analyzed and compared using the dChip software ( http://www.hsph.harvard.edu/~cli/complab/dchip/) ID_REF =
VALUE = dChip normalized signal Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF SDRF File E-GEOD-21765.sdrf.txt Term Source Name EFO Term Source File http://www.ebi.ac.uk/efo/ Term Source Version