{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Junya Mizoi"],"study_type":["transcription profiling by array"],"organism":["Solanum lycopersicum"],"species":["Solanum lycopersicum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16410"],"description":["Coral sand–based hydroponic cultivation of tomato can increase fruit sugar content while minimizing yield loss. To investigate the physiological effects of coral sand on tomato plants, we compared gene expression profiles in seedling leaves grown on standard coconut peat medium (control) with those grown on coral sand as the solid substrate."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Leaf blades were cut from the plants, and the samples were frozen in liquid nitrogen.","Growth Protocol - Tomato seedlings were transplanted at the age of 4 w old and grown for 2 w hydroponically with coconut peat (control) or coral sand in a greenhouse.","Nucleic Acid Extraction - Total RNA was isolated from the frozen samples using RNA iso plus (TaKaRa). Three seedlings were pooled to prepare an RNA sample.","Hybridization - Two sets of samples (biological repeats) were analyzed using a Cy3 and Cy5 dye swap (technical repeats).","Labeling - Total RNA (250 ng) was labeled with a Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.","Scaning - Microarray slides were scanned (scanner model G2505C with scan control software, version A.8.4; Agilent Technologies) and the data were analyzed using Feature Extraction software, version 11.5.1.1 (Agilent technologies) using the default settings."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Junya Mizoi"],"data_protocol":["Data Transformation - Data was processed using the Subio Platform software. Normalization was done by selecting LOWESS Normalization. One representative probe was selected for each locus."],"additional_accession":[]},"is_claimable":false,"name":"Microarray analysis of tomato leaves grown hydroponically with coral sand as the solid medium","description":"Coral sand–based hydroponic cultivation of tomato can increase fruit sugar content while minimizing yield loss. To investigate the physiological effects of coral sand on tomato plants, we compared gene expression profiles in seedling leaves grown on standard coconut peat medium (control) with those grown on coral sand as the solid substrate.","dates":{"release":"2026-01-06T00:00:00Z","modification":"2026-05-27T16:10:21.558Z","creation":"2025-12-18T15:53:15.331Z"},"accession":"E-MTAB-16410","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003815"]}}