ArrayExpressapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1625/E-MTAB-1625.sdrf.txtftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1625/E-MTAB-1625.idf.txtprimaryOK20002200TranscriptomicsMaria C KeaysSamuel E FoxIllumina HiSeq 2000Oryza Sativa Japonica GroupRNA-seq of coding RNAhttps://www.ebi.ac.uk/arrayexpress/experiments/E-MTABfirstname.lastname@example.org@ebi.ac.ukArrayExpressGrowth Protocol - Oryza sativa L. japonica nipponbare seedlings were grown in growth chambers to the 2-3 leaf stage. At 2 weeks old, they were subjected to salt stress treatment by watering with 300 mM NaCl solution (or normal watering for control plants). Treatment was applied at 10:00 PST (2 hours post-dawn). Seedling shoots (stem and leaves) were sampled at 1 hour, 5 hours, and 24 hours post-treatment.
Library Construction - Libraries were prepared using the TruSeq(TM) RNA Sample Preparation Kits (v2).
Nucleic Acid Extraction - Total cellular RNA was extracted using RNA Plant Reagent (Life Technologies) and treated with RNase-free Turbo DNase (Life Technologies) followed by a clean-up step using Plant RNeasy kits (Qiagen). Concentration, integrity and extent of contamination by ribosomal RNA were assessed using ND-1000 spectrophotometer (Thermo Fisher Scientific) and Bioanalyzer 2100 (Agilent Technologies). For details see Fox et al. (2009) Applications for Ultra-high-Throughput Sequencing. In: Belostotsky (ed.), Plant Systems Biology, vol. 553, pp. 79--108.
Sequencing - Libraries were sequenced on the Illumina HiSeq 2000 instrument (Illumina Inc).2020extent, tspst1, Ribonucleic, Salinity Stresses, phenol sulfotransferase activity, Stp, Pflanze, instrument configuration, ribosomal RNA, Reponse, HiSeq 2000, CG11121, viridiplantae, Stp1, old, halite, exact), GRP1, stp, Grp1, Salt Stress Response, primary stem, Non Polyadenylated, RNA Gene Products, treatment, average, Malted Grain, Grain, reference sample, Biology, entire life cycle, PTPSTEP, Salt, Salt Stresses, nucleic acid library preparation, HardwareType, Ribosomal RNA, plants, 3'-phosphoadenylyl-sulfate:phenol sulfotransferase activity, SO, free, EG:196F3.2, cloruro sodico, salt, h, DNAse, Reaction, l(2)k08110, Sprouted, disease management, stage, Salinity Stress Reponse, Asian cultivated rice, So, reagents, GPH, degree of contamination, rock salt, ritodrine sulfotransferase activity, ribose nucleic acid, completeness, land plants, ribonucleic acids, aryl sulphotransferase activity, Normalcy, Oryza sativa cultivar Nipponbare, Salinity Stress Reaction, Plant Sprouts, common salt, Ribonukleinsaeure, 126.96.36.199, 15S, red rice, PST, pentosenucleic acids, Ribonucleic acids, Seed, ST1A1, CG14784, Nipponbare, reactif, Acid, Turbo <subgenus>, Seeds, Stress Response, growth pattern, ribosomal protein, instrument, Step, CG11628, non-developmental growth, life, pst, Plant, reagent, Striatum-enriched protein-tyrosine phosphatase, natrii chloridum, 葉 (Japanese, Salinity Stress Reponses, Seedling, Grains, Health, higher plants, primary axis, STEP, rice, Salt Stress Reactions, DmelCG32810, Salinity Stress Reactions, Plant Sprout, lifespan, GRP1/cytohesin 1, developmental stage, Salinity Stress, stalk, sulfokinase activity, hardware, CG11633, cytohesin/GRP1, DmelCG11121, Salt Stress Reaction, Sprouted Seed, Gene Products, Malted, Normalities, 1-naphthol phenol sulfotransferase activity, plantae, somda, reactivo, entire lifespan, dopamine sulfotransferase activity, chlorure de sodium, nucleic acid library construction, l(2)SH2 0323, Turbo <genus>, Salt Stress, culm, Solution, ribosomal ribonucleic acid, CG14783., Non-Polyadenylated RNA, Neural-specific protein-tyrosine phosphatase, st1a3, Stress Reaction, Kochsalz, 2-naphtholsulfotransferase activity, CG8588, Controlled, Drl, 4-nitrocatechol sulfokinase activity, Controlling, RNA, Malted Grains, axis, Oryza sativa Nipponbare, Dm-65, stepk, RNS, arylsulfotransferase, Sprout, Mdu, p-nitrophenol sulfotransferase activity, INSDC_feature:rRNA, Natriumchlorid, mda, yeast nucleic acid, Systems, table salt, 15S RNA, NaCl, membrane bound ribosome, l(2)SH0323, Library, ami, free ribosome, CYH1, ribonucleic acid, Sprouts, DmelCG8588, Normality, library construction, med, Non Polyadenylated RNA, Oryza sativa, Non-Polyadenylated, stp1, INSDC_qualifier:unknown, Stress Reponse, Ribonucleic Acid, hoja (Spanish, DmelCG11628, red rice <Oryza sativa>, concentration, Stress, Sprouted Seeds, Salinity, Response, phenol sulfokinase activity, AI266890, Salt Stress Responses, CG32810, sodium chlorideSalinity Stresses, Stress Response, Effects, Longterm, Salinity Stress, Oryza sativa Nipponbare, Longterm., Oryza sativa, Salt, Salt Stresses, Longterm Effect, Stress Reponse, Reponse, Long-Term, Oryza sativa cultivar Nipponbare, Salt Stress, Long Term, Longterm Effects, Salinity Stress Reaction, Salinity Stress Reponses, period, red rice <Oryza sativa>, Stress Reaction, rice, Reaction, Salt Stress Reaction, Stress, Long Term Effects, Salt Stress Reactions, Salinity, red rice, Response, Salt Stress Response, Salt Stress Responses, Long-Term Effect, Salinity Stress Reponse, Salinity Stress Reactions, Nipponbare, Effect, Long-Term Effects, time, Asian cultivated riceWater, Plant Sprout, Salinity Stresses, Materials, Effects, Salinity Stress, Gene, BOUND WATER, RNA-seq., Reponse, oxidane, Long Term, WATER, agua, HOH, period, halite, Salt Stress Reaction, Sprouted Seed, Salt Stress Response, Whole Transcriptome Shotgun Sequencing, Malted, Effect, treatment, Malted Grain, Grain, Genetic, Longterm, Salt, Salt Stresses, chlorure de sodium, eau, Long-Term, Salt Stress, cloruro sodico, salt, h, Stress Reaction, Reaction, Sprouted, Kochsalz, disease management, dihydridooxygen, Long-Term Effect, Salinity Stress Reponse, dihydrogen oxide, Long-Term Effects, Asian cultivated rice, rock salt, Malted Grains, Data Set, Oryza sativa Nipponbare, aqua, Longterm Effect, Sprout, Cistrons, Oryza sativa cultivar Nipponbare, results, Salinity Stress Reaction, H2O, Plant Sprouts, common salt, Natriumchlorid, water, Long Term Effects, red rice, Genetic Materials, table salt, Seed, NaCl, Nipponbare, Genetic Material, Hydrogen Oxide, Seeds, Sprouts, Stress Response, Oryza sativa, Plant, hydrogen hydroxide, Stress Reponse, natrii chloridum, acqua, Longterm Effects, Salinity Stress Reponses, Seedling, Grains, red rice <Oryza sativa>, Material, rice, Stress, Sprouted Seeds, Salt Stress Reactions, Salinity, Response, Cistron, Salt Stress Responses, Wasser, [OH2], Salinity Stress Reactions, time, sodium chloride0.00.00.02.970444081390168E-40.006169031462060457trueRNA-seq of coding RNA in rice (Oryza sativa L. Japonica nipponbare) under salt stress over a time-course, Gramene projectOryza sativa L. Japonica nipponbare seedlings were treated with 300mM NaCl or water, and then samples were taken after one hour, five hours and 24 hours, to assess which genes are differentially expressed over time during salt stress treatment. The results from this dataset are also compared with those from the same samples assayed using RNA-seq.2015-08-252015-08-25E-MTAB-162539947