{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Regine Kahmann"],"study_type":["transcription profiling by array"],"organism":["Zea mays"],"species":["Zea mays"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-48536"],"description":["Anthocyanin induction in plant is considered a general defense response against biotic and abiotic stresses. The infection by Ustilago maydis, the corn smut pathogen, is accompanied with anthocyanin induction in leaf tissue. We revealed that anthocyanin is intentionally induced by the virulence promoting secreted effector protein Tin2. Tin2 protein functions inside plant cells where it interacts with cytoplasmic maize protein kinase ZmTTK1. Tin2 masks an ubiquitin-proteasome degradation motif in ZmTTK1 leading to a more stable active kinase. Active ZmTTK1 controls transcriptional activation of genes in the anthocyanin biosynthesis pathway rerouting phenylalanine away from lignin biosynthesis. Therefore, we performed microarray analysis to understand how maize gene transcription in phenylpropanoid pathway is differentially changed after infection with Ustilago maydis SG200 (wild type) and SG200Dtin2 (anthocyanin-inducing effector mutant). We prepared three biological replicates for mock-inoculated maize (control), SG200-infected maize and SG200M-NM-^Ttin2-infected maize. For 1 sample, we harvested the leaves (1-3cm below injection hole) from 20 plants and pooled them. At 4 days post inoculation, total RNA was extracted."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Fungus infected or water-inoculated tissue from 20 plants per experiment was harvested at 4 dpi by excising a section of the third leaf between 1 and 3 cm below the injection holes. For RNA extraction, material was pooled, ground to powder under liquid nitrogen and RNA was extracted with Trizol reagent (Invitrogen). RNA was purified applying the RNeasy kit (Qiagen).","Sample Treatment - 7-day-old maize young seedlings were infected with U. maydis cell suspensions (OD600=3.0).","Hybridization - Affymetrix protocols (GeneChipM-. Hybridization Wash and Stain Kit; Midi_Euk2V3 protocol on GeneChip Fluidics Station 450)","Growth Protocol - Maize plants (Early Golden Bantam) were grown in a phytochamber in a 15 h/9 h light/dark cycle; light period started/ended with 1 h ramping of light intensity. Temperature was 28 and 20 M-0C, relative humidity 40% and 60% during light and dark periods, respectively, with 1 h ramping for both values. Plants were inoculated with H2O (mock), SG200 and SG200M-NM-^Ttin2","Labeling - Affymetrix protocols (GeneChipM-. Hybridization Wash and Stain Kit)","Scaning - Affymetrix protocols (scanning on Affymetrix GSC3000G)"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Shigeyuki Tanaka","Nina Neidig","Regine Kahmann"],"data_protocol":["Data Transformation - Partek Genomics SuiteM-BM-. version 6.12. Expression values were normalized using the RMA method. ID_REF =  VALUE = RMA signal intensity"],"additional_accession":[]},"is_claimable":false,"name":"Maize gene expression after infection of Ustilago maydis SG200 and SG200M-NM-^Ttin2","description":"Anthocyanin induction in plant is considered a general defense response against biotic and abiotic stresses. The infection by Ustilago maydis, the corn smut pathogen, is accompanied with anthocyanin induction in leaf tissue. We revealed that anthocyanin is intentionally induced by the virulence promoting secreted effector protein Tin2. Tin2 protein functions inside plant cells where it interacts with cytoplasmic maize protein kinase ZmTTK1. Tin2 masks an ubiquitin-proteasome degradation motif in ZmTTK1 leading to a more stable active kinase. Active ZmTTK1 controls transcriptional activation of genes in the anthocyanin biosynthesis pathway rerouting phenylalanine away from lignin biosynthesis. Therefore, we performed microarray analysis to understand how maize gene transcription in phenylpropanoid pathway is differentially changed after infection with Ustilago maydis SG200 (wild type) and SG200Dtin2 (anthocyanin-inducing effector mutant). We prepared three biological replicates for mock-inoculated maize (control), SG200-infected maize and SG200M-NM-^Ttin2-infected maize. For 1 sample, we harvested the leaves (1-3cm below injection hole) from 20 plants and pooled them. At 4 days post inoculation, total RNA was extracted.","dates":{"release":"2014-01-28T00:00:00Z","modification":"2023-09-06T00:49:52.869Z","creation":"2022-01-28T18:01:55.633Z"},"accession":"E-GEOD-48536","cross_references":{"GEO":["GSE48536"],"EFO":["EFO_0002768"]}}