{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Todsapol Techo"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"organism":["Oryza sativa Indica Group"],"species":["Oryza sativa Indica Group"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16540"],"description":["This dataset comprises paired-end RNA-sequencing of Oryza sativa L. cv. KDML105 seedling leaves were collected at seven time points (0, 4, 8, 12, 16, 20, and 24 hours) following treatment with 150 mM NaCl or control conditions. The experimental design captures transcriptomic dynamics across a complete 24-hour diurnal cycle under 12:12 hour light:dark photoperiod, with two biological replicates per condition and time point (28 samples total). This study elucidates the temporal integration of circadian regulatory networks with salt stress responses in a salt-sensitive rice cultivar relevant to Southeast Asian agriculture."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Fully expanded leaves were harvested at seven time points post-treatment: 0.5, 4, 8, 12, 16, 20, and 24 h (ZT4.5, ZT8, ZT12, ZT16, ZT20, ZT0, ZT4). Each biological replicate comprised 3-5 pooled leaves flash-frozen in liquid nitrogen and stored at -80°C. Two biological replicates per condition per time point yielded 28 total samples (2 conditions × 7 time points × 2 replicates).","Sample Treatment - Twenty-one-day-old seedlings were exposed to 150 mM NaCl in full-strength Yoshida's solution or control conditions (Yoshida's solution without NaCl). Treatment commenced at 10:00 (ZT4) and continued for 24 h under established photoperiod conditions. Environmental conditions maintained greenhouse parameters (19-33°C, 91% RH).","Sequencing - Pooled libraries were sequenced on NovaSeq 6000 platform (Illumina) using S4 Reagent Kit v1.5 in 2×150 bp paired-end configuration.","Growth Protocol - KDML105 rice seeds (Oryza sativa L. cv. KDML105) were surface-sterilized, germinated on moistened tissue for 48 h, and transferred to reverse osmosis water for 72 h under 12/12 h light/dark photoperiod (light onset 06:00, ZT0). Seedlings were cultivated in half-strength Yoshida's solution for 96 h, then transferred to full-strength Yoshida's solution until reaching 21-day-old seedling stage (three-leaf stage). Nutrient medium was refreshed every 96 h. Cultivation occurred in greenhouse conditions at Department of Biology, Khon Kaen University (temperature range 19-33°C, relative humidity 91% average)","Library Construction - Libraries were constructed using VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme Biotech) with poly(A) selection via VAHTS mRNA Capture Beads from 1-2 μg total RNA. mRNA underwent heat fragmentation (94°C, 5-7 min, median 200-300 nt), followed by dUTP-based strand-specific cDNA synthesis, end-repair, A-tailing, and dual-indexed adapter ligation. After UDG treatment removing marked second strand, libraries were PCR-amplified (12-15 cycles) and size-selected (250-450 bp) using AMPure XP beads (0.6-1.0× ratio). Quality control employed Bioanalyzer and Qubit quantification. Libraries meeting quality criteria (single peak 300-400 bp, <5% adapter dimers, ≥5 nM) were normalized and pooled.","Nucleic Acid Extraction - Total RNA was extracted from ~100 mg frozen leaf tissue using RNeasy Plant Mini Kit (Qiagen) with on-column DNase I treatment. Quality assessment employed NanoDrop spectrophotometry (A260/A280 ≥ 2.0, A260/A230 ≥ 2.0) and 4200 TapeStation (RIN ≥ 6.0). Samples were stored at -80°C until library preparation."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Todsapol Techo"],"additional_accession":[]},"is_claimable":false,"name":"Time-series transcriptomic analysis of salt stress response under diurnal cycle in Thai jasmine rice (Oryza sativa L. cv. KDML105) seedling leaves","description":"This dataset comprises paired-end RNA-sequencing of Oryza sativa L. cv. KDML105 seedling leaves were collected at seven time points (0, 4, 8, 12, 16, 20, and 24 hours) following treatment with 150 mM NaCl or control conditions. The experimental design captures transcriptomic dynamics across a complete 24-hour diurnal cycle under 12:12 hour light:dark photoperiod, with two biological replicates per condition and time point (28 samples total). This study elucidates the temporal integration of circadian regulatory networks with salt stress responses in a salt-sensitive rice cultivar relevant to Southeast Asian agriculture.","dates":{"release":"2026-08-28T00:00:00Z","modification":"2026-08-28T11:11:03.365Z","creation":"2026-01-16T18:33:16.208Z"},"accession":"E-MTAB-16540","cross_references":{"ENA":["ERP187672"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0004184","EFO_0003969"]}}