{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Junya Mizoi"],"organism":["Solanum lycopersicum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16436"],"description":["Gene expression changes in developing tomato fruits in response to high salinity, low-phosphate conditions, and their combination were analyzed under hydroponic cultivation. RNA was extracted from pericarp tissue of fruits at 5 and 15 days after pollination, and gene expression profiles were compared by RNA-seq."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Pericarp tissues were separated from fruits using a scalpel, and the samples were frozen in liquid nitrogen.","Growth Protocol - Tomato seedlings were grown hydroponically with different concentrations of nutrients and salts. EC12, P10 and EC12 refers to a high salt condition (EC12, 94 mM NaCl), a low phosphate solution (10% of control) and the combination of both.","Library Construction - Library was constructed as described in Lasy-seq protocol (https://sites.google.com/view/lasy-seq/)","Sequencing - Nucleic acid sequencing was performed as described in Lasy-seq protocol (https://sites.google.com/view/lasy-seq/).","Nucleic Acid Extraction - Samples were ground in liquid nitrogen into powder. Total RNA was isolated from the powdered samples using RNA iso plus (TaKaRa). One sample is from one fruit."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Original read data were quality-filtered using fastp (v0.21.1) and aligned to the Solanum lycopersicum ITAG4.0 cDNA reference with Bowtie (v1.2.3). Transcript and gene expression levels were quantified using RSEM (v1.3.1) based on an expectation–maximization algorithm. Expression values were normalized as TPM and FPKM. Transcript-level alignments were processed using samtools (v1.9)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Solanum lycopersicum"],"pubmed_authors":["Junya Mizoi"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic profiling of immature tomato fruits grown hydroponically under high salt, low-phosphate and their combination","description":"Gene expression changes in developing tomato fruits in response to high salinity, low-phosphate conditions, and their combination were analyzed under hydroponic cultivation. RNA was extracted from pericarp tissue of fruits at 5 and 15 days after pollination, and gene expression profiles were compared by RNA-seq.","dates":{"release":"2026-01-06T00:00:00Z","modification":"2026-05-31T07:20:20.734Z","creation":"2025-12-19T15:55:54.074Z"},"accession":"E-MTAB-16436","cross_references":{"ENA":["ERP186846"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}