{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Gunther Doehlemann"],"organism":["Zea mays"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-28479"],"description":["Ustilago maydis is a basidiomycete fungus that causes smut disease in maize. Most prominent symptoms of the disease are plant tumors, which can be induced by U. maydis on all aerial parts of the plant. We identified two linked genes, pit1 and pit2, which are specifically expressed during plant colonization. Deletion mutants for either pit1 or pit2 are unable to induce tumor development and elicit plant defense responses. We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to deletion pit1 and pit2 mutants and found plant responses to both mutants being not significantly distinguishable. U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200Dpit1 and SG200Dpit2, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023, 4d mock and 4d SG200 Samples, equivalent record in Arrayexpress: E-GEOD-10023). These data served as controls for this experiment."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol Midi_Euk2V3.","Scaning - GeneChips were scanned on a Affymetrix GSC3000G scanner","Growth Protocol - Maize plants (Early Golden Bantam) were grown in a phytochamber in a 15/9 hour light/dark cycle. Temerature was 28°c and 20°c, relative humudity 40% and 60% during light and dark periods, respectively, with 1 hour ramping for both parameters.","Nucleic Acid Extraction - Trizol extraction of total RNA was performed according to the manufacturer's instructions.","Scaning - Date were analyzed with the GeneChip operating software (GCOS) 1.4 to generate CEL files.","Sample Treatment - Seedlings were inoculated 7 days after sawing with the respective U. maydis strains, resulting in an infection of the third seedling leaf. Samples were taken 4 days after fungal infection.","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","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - ID_REF = <br>VALUE = Signal<br>ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M)<br>DETECTION P-VALUE ="],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Ustilago maydis is a biotrophic fungal pathogen that colonizes living tissue of its host plant maize. Based on transcriptional upregulation during biotrophic development we identified the pit (proteins important for tumours) cluster, a novel gene cluster comprising four genes of which two are predicted to encode secreted effectors. Disruption of the gene cluster abolishes U. maydis-induced tumour formation and this phenotype can be caused by deleting either pit1 encoding a transmembrane protein or pit2 encoding a secreted protein. Pit1 localizes to the fungal plasma membrane at hyphal tips, endosomes and vacuoles while Pit2 is secreted to the biotrophic interface. Both Δpit1 and Δpit2 mutants are able to penetrate maize epidermis and grow intracellularly at sites of infection but fail to spread in the infected leaf. Microarray analysis shows an indistinguishable response of the plant to infection by Δpit1 and Δpit2 mutant strains. Transcriptional activation of maize defence genes in infections with Δpit1/2 mutant strains indicates that the mutants have a defect in suppressing plant immune responses. Our results suggest that the activity of Pit1 and Pit2 during tumour formation might be functionally linked and we discuss possibilities for a putative functional connection of the two proteins."],"study_type":["transcription profiling by array"],"species":["Zea mays"],"pubmed_title":["Two linked genes encoding a secreted effector and a membrane protein are essential for Ustilago maydis-induced tumour formation"],"pubmed_authors":["Doehlemann G, Reissmann S, Assmann D, Fleckenstein M, Kahmann R","Gunther Doehlemann","Stefanie Reissmann","Regine Kahmann"],"additional_accession":[]},"is_claimable":false,"name":"Maize gene expression during infection with Ustilago maydis strains SG200Dpit1 and SG200Dpit2","description":"Ustilago maydis is a basidiomycete fungus that causes smut disease in maize. Most prominent symptoms of the disease are plant tumors, which can be induced by U. maydis on all aerial parts of the plant. We identified two linked genes, pit1 and pit2, which are specifically expressed during plant colonization. Deletion mutants for either pit1 or pit2 are unable to induce tumor development and elicit plant defense responses. We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to deletion pit1 and pit2 mutants and found plant responses to both mutants being not significantly distinguishable. U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200Dpit1 and SG200Dpit2, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023, 4d mock and 4d SG200 Samples, equivalent record in Arrayexpress: E-GEOD-10023). These data served as controls for this experiment.","dates":{"release":"2011-07-01T00:00:00Z","modification":"2023-08-12T17:04:41.384Z","creation":"2022-03-07T01:59:54.134Z"},"accession":"E-GEOD-28479","cross_references":{"GEO":["GSE28479"],"pubmed":["21692877"],"EFO":["EFO_0002768"],"doi":["10.1111/j.1365-2958.2011.07728.x"]}}