{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Gunther Doehlemann"],"organism":["Zea mays"],"software":["MicroArraySuite 5.0"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-12892"],"description":["The basidiomycete Ustilago maydis causes smut disease in maize. Colonization of the host plant is initiated by direct penetration of cuticle and cell wall of maize epidermis cells. The invading hyphae are surrounded by the plant plasma membrane and proliferate within the plant tissue. We identified a novel secreted protein, termed Pep1. Disruption mutants of pep1 are not affected in saprophytic growth and develop normal infection structures. However, Δpep1 mutants fail to penetrate the epidermal cell wall and elicit a strong plant defense response. Using Affymetrix maize arrays we identified about 110 plant genes which are differentially regulated in Δpep1 and wild type infections during the penetration stage. Experiment Overall Design: In three independent experiments plants were infected with the strain SG200Dpep1 which is derived from the solopathogenic U. maydis strain SG200. Samples from infected leaves were taken at  24 hours post infection. Samples were treated under the same conditions as described previosly (Doehlemann et al. (2008) Plant J, in press)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Processing - U. maydis strain SG200Dpep1 was grown in liquid culture overnight to an OD600 of 1.0, harvested by centrifugation, and resuspended in water to an OD600 of 3.0; compatible strains were mixed in equal amounts immediately before infection; 0.2 ml of cell suspension mixes were injected into the leaf whorl of 6â€\"7-day-old corn plants (as described in Mol Microbiology 42:1047-1063). Plants were infected 7 days after sowing 1 h before end of the light period with the exception of the 12 hpi samples were plants were infected during the beginning of the light period.","Sample Processing - U. maydis strain SG200 (Nature 444:97-101) was grown in liquid culture overnight to an OD600 of 1.0, harvested by centrifugation, and resuspended in water to an OD600 of 3.0; compatible strains were mixed in equal amounts immediately before infection; 0.2 ml of cell suspension mixes were injected into the leaf whorl of 6â€\"7-day-old corn plants (as described in Mol Microbiology 42:1047-1063). Plants were infected 7 days after sowing 1 h before end of the light period with the exception of the 12 hpi samples were plants were infected during the beginning of the light period.","Hybridization - Title: Affymetrix Generic Hybridization. Description:","Nucleic Acid Extraction - For RNA isolation, material from 30 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer’s instructions, respectively.","Growth Protocol - Maize plants of the cultivar Early Golden Bantam were grown in a phytochamber in a 15 h / 9 h light-dark cycle; light period started with a  continuous increase from 0% to 100% light for 1h, and ended 13h later with a continuous decrease from 100% to 0% light for 1 h. Temperature was 28°C and 20°C, relative humidity 40% and 60% during light and dark periods, respectively, with a 1 h ramping for both values. Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) to avoid shading of the plants.","Growth Protocol - Maize plants of the cultivar Early Golden Bantam were grown in a phytochamber in a 15 h / 9 h light-dark cycle; light period started with a continuous increase from 0% to 100% light for 1h, and ended 13h later with a continuous decrease from 100% to 0% light for 1 h. Temperature was 28°C and 20°C, relative humidity 40% and 60% during light and dark periods, respectively, with a 1 h ramping for both values. Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) to avoid shading of the plants.","Labeling - Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","Additional Files","MAGE-TAB Files","Array Designs"],"data_protocol":["Assay Data Transformation - Title: Affymetrix CHP Analysis (ExpressionStat). Description:","Feature Extraction - Title: Affymetrix CEL analysis. Description:"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"study_type":["transcription profiling by array"],"species":["Zea mays"],"pubmed_authors":["Gunther Doehlemann"],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling of maize n during infection with Ustilago maydis strain SG200Dpep1","description":"The basidiomycete Ustilago maydis causes smut disease in maize. Colonization of the host plant is initiated by direct penetration of cuticle and cell wall of maize epidermis cells. The invading hyphae are surrounded by the plant plasma membrane and proliferate within the plant tissue. We identified a novel secreted protein, termed Pep1. Disruption mutants of pep1 are not affected in saprophytic growth and develop normal infection structures. However, Δpep1 mutants fail to penetrate the epidermal cell wall and elicit a strong plant defense response. Using Affymetrix maize arrays we identified about 110 plant genes which are differentially regulated in Δpep1 and wild type infections during the penetration stage. Experiment Overall Design: In three independent experiments plants were infected with the strain SG200Dpep1 which is derived from the solopathogenic U. maydis strain SG200. Samples from infected leaves were taken at  24 hours post infection. Samples were treated under the same conditions as described previosly (Doehlemann et al. (2008) Plant J, in press).","dates":{"release":"2008-10-25T00:00:00Z","modification":"2022-11-26T17:34:31.074Z","creation":"2022-02-23T18:59:06.659Z"},"accession":"E-GEOD-12892","cross_references":{"GEO":["GSE12892"],"EFO":["EFO_0002768"]}}