Investigation Title Hanley-Bowdoin ArabidopsisCaLCuV 12dpi Comment[Submitted Name] Hanley-Bowdoin ArabidopsisCaLCuV 12dpi Experimental Design pathogenicity_design co-expression_design transcription profiling by array Experimental Design Term Source REF mo mo EFO Comment[AEExperimentType] transcription profiling by array Comment[AEExperimentDisplayName] Transcription profiling by array of Arabidopsis infected with geminivirus Cabbage leaf curl virus Comment[ArrayExpressReleaseDate] 2008-07-30 Comment[AEMIAMESCORE] 5 Comment[ArrayExpressAccession] E-ATMX-34 Comment[MAGETAB TimeStamp_Version] 2010-07-29 14:33:47 Last Changed Rev: 13058 Experimental Factor Name infect Experimental Factor Type infect Experimental Factor Term Source REF Person Last Name Ascencio-Ibanez Person First Name Trino Person Mid Initials Person Email trino_ascencio@ncsu.edu Person Phone 919 5155736 Person Fax 919 5131209 Person Address "CB7651, Partners III Rm B04" Person Affiliation Molecular and Structural Biochemistry 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 2008-07-30 PubMed ID 18650403 Publication DOI 18650403 Publication Author List "Ascencio-Ibanez, Jose Trinidad; Sozzani, Rosangela; Lee, Tae-Jin; Chu, Tzu-Ming; Wolfinger, Russell D.; Cella, Rino; Hanley-Bowdoin, Linda" Publication Title Global Analysis of Arabidopsis Gene Expression Uncovers a Complex Array of Changes Impacting Pathogen Response and Cell Cycle during Geminivirus Infection Publication Status journal_article Publication Status Term Source REF The MGED Ontology Experiment Description Effect of geminivirus Cabbage leaf curl virus on Arabidopsis Col-0 at 12 days post-inoculation during short day conditions. Protocol Name P-CAGE-26718 P-CAGE-26721 P-CAGE-26719 P-CAGE-26720 P-AFFY-2 Affymetrix:Protocol:Hybridization-Unknown P-AFFY-6 Affymetrix:Protocol:ExpressionStat Protocol Type grow specified_biomaterial_action pool nucleic_acid_extraction labeling hybridization feature_extraction bioassay_data_transformation Protocol Description "Arabidopsis (Arabidopsis thaliana) Col-0 plants were grown on Metro-Mix 360 (SunGro) at 20°C in a Percival reach-in chamber (Series 101 without humidity controls) with a 8/16-h light/dark cycle under a light intensity of 17,000 Lux. For microarray experiments, plants with 16-18 true leaves were co-inoculated with Agrobacterium tumefaciens (strain A208::pTiC58-BI) transformed with pNSB1090 or pNSB1091, which contain T-DNAs with partial tandem copies of wild type CaLCuV A and B components, respectively (Egelkrout et al., 2002). The Agrobacterium transformants were inoculated from glycerol stocks (20 µl) and grown individually to saturation in Luria broth (LB) supplemented with 75 mg/mL spectinomycin at 28ºC overnight and then mixed 1:1. A drop of the mixed culture was deposited directly onto a wounded area generated by puncturing the rosette center 10 times with a 25 gauge needle. The meristematic region was avoided during the wounding process. Control plants were mock-inoculated using the same Agrobacterium strain transformed with pNSB690, which contains a 35S promoter uidA expression cassette. Typically, 12 plants were inoculated with CaLCuV while 6 were mock inoculated per tray. The tray was covered with a clear plastic lid for 4 days and then uncovered for the remainder of the growth period. Symptoms were monitored from the first day post-inoculation (dpi) until the CaLCuV-infected plants were dead at 6 weeks post infection. " "Plants with 16-18 true leaves were co-inoculated with Agrobacterium tumefaciens (strain A208::pTiC58-BI) transformed with pNSB1090 or pNSB1091, which contain T-DNAs with partial tandem copies of wild type CaLCuV A and B components, respectively. The Agrobacterium transformants were inoculated from glycerol stocks (20 µl) and grown individually to saturation in Luria broth (LB) supplemented with 75 mg/mL spectinomycin at 28ºC overnight and then mixed 1:1. A drop of the mixed culture was deposited directly onto a wounded area generated by puncturing the rosette center 10 times with a 25 gauge needle. The meristematic region was avoided during the wounding process. Control plants were mock-inoculated using the same Agrobacterium strain transformed with pNSB690, which contains a 35S promoter uidA expression cassette. " "Leaves 7-9 at 12 days post-inoculation were harvested, pooled, flash frozen, ground in liquid nitrogen and stored at –80ºC. Three biological replicas corresponding to infected and mock-inoculated samples were collected and processed independently. Each replica contains 6 plants for mock-inoculated samples and 12 for virus-inoculated samples." Total RNA was extracted from each sample using the Plant RNeasy Mini Kit (Qiagen). Title: Affymetrix in vitro transcription. Description: Title: Affymetrix Generic Hybridization. Description: Title: Affymetrix CEL analysis. Description: Title: Affymetrix CHP Analysis (ExpressionStat). Description: Protocol Parameters light source;media;night temperature;night humidity;light hours;light intensity;day temperature;day humidity; Extracted product;Amplification; Protocol Hardware Protocol Software MicroArraySuite 5.0 MicroArraySuite 5.0 MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF The MGED Ontology mo The MGED Ontology SDRF File E-ATMX-34.sdrf.txt Term Source Name NCBI Taxonomy The MGED Ontology ArrayExpress mo 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://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version