{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Kyonoshin Maruyama"],"study_type":["transcription profiling by array"],"organism":["Oryza sativa"],"species":["Oryza sativa"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13217"],"description":["We conducted an oligo microarray analysis to investigate the gene transcripts in the roots of NB and DJ123 grown in LS and control soils."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Harvest plants and move plants in liquid N2 as soon as possible (sub- 10 seconds). Transfer the frozen plants (150-300 mg) to a mortar containing liquid N2 and grind to a very fine powder using pestle. The plants can be kept frozen during grinding by the addition of liquid N2. Transfer the powdered plants (~100 mg) into a pre-cooled (in liquid N2) 2 ml eppendorf tube using pre-cooled spatula and move each sample tube in liquid N2.","Growth Protocol - Two rice (Oryza sativa L.) varieties—DJ123 and Nipponbare (NB)—were used in this study. For all experiments under soil conditions, rice plants were grown in 200-ml plastic pots, which were filled with one of the two rice varieties. For the control treatment, sulfur was applied as sodium sulfate at a rate of 0.02 g pot–1. Under both the LS and control conditions, N, P2O5, and K2O were supplemented by the addition of urea, sodium phosphate, and potassium chloride, respectively, at a rate of 0.1 g of each per pot.","Hybridization - Add 600 ng of cyanine 3-labeled, linearly amplified cRNA linearly amplified cRNA, 5 μl of diluted 10X Blocking Agent and 1 μl of 25X Fragmentation Buffer and gently mix by pipetting. Prepare the reactions for a total volume of 25 μl. Incubate at 60°C for exactly 30 minutes to fragment RNA. Move the reactions on ice and incubate for 60 seconds. Add 25 μl of 2X GEx Hybridization Buffer HI-RPM to stop the fragmentation reaction and mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix using vortex mixer. Centrifuge at 12,000 g for 60 seconds at room temperature to drive down tube contents from the tube walls and lid. Use immediately. Do not store. Move sample on ice and load onto the array as soon as possible. Load a clean gasket slide into the Agil","Nucleic Acid Extraction - After N2 evaporates, add 1 m1 of RNAiso Plus to each sample tube and mix well using micro tube mixer for 5-10 minutes. Centrifuge at 12,000 g for 15 minutes at 4°C and transfer 800 μl of supernatant to a new tube. Add chloroform (200-400 μl) to each sample tube and mix well using micro tube mixer for 5 minutes at room temperature. Centrifuge at 12,000 g for 10 minutes at 4°C and transfer 400 μl the top layer to a new tube. Add 250 μl of high salt buffer and 250 μl of isopropanol to each sample tube and mix well using micro tube mixer for 5 minutes at room temperature. Centrifuge at 12,000 g for 10 minutes at 4°C and after removal of supernatant carefully, dissolve in 100 μl of ultrapure water. Add 10 μl of sodium acetate and 250 μl of 99.5% (v/v) ethanol to each s","Labeling - Prepare 200 ng/1.5 μl of diluted total RNA, 2 μl of final diluted Spike mixture and 1.8 μl of diluted T7 promoter primer mixture in a 0.2 ml microcentrifuge tube. Each tube now contains a total volume of 5.3 μl. Incubate reactions in a thermal cycler for 10 minutes at 65°C to denature the primer and the RNA sample. Move the reactions on ice and incubate for 5 minutes and spin each sample briefly to drive down tube contents from the tube walls and lid. Add 4.7 μl of cDNA master mixture to each sample tube and mix by pipetting up and down and incubate reactions at 40°C in a thermal cycler for 2 hours. Each tube now contains a total volume of 10 μl. Incubate reactions in a thermal cycler for 15 minutes at 70°C to inactivate the AffinityScript enzyme. Move reactions to ice and incub","Scaning - Put assembled slide holders into the scanner carousel. In the Scan Control main window, choose the slot number of the first slide for Start Slot and the slot number for the last slide for End Slot. For 8x60K microarrays, select Profile AgilentG3_GX_2Color. In the Scan Control main window, click Scan Slot m-n where m is the slot of the first slide, and n is the slot for the last slide. Open the Agilent Feature Extraction (FE) software and open the images (.tif). Save the FE Project (.fep) by selecting File > Save As and browse for desired location > Start Extracting. After the extraction is completed successfully, view the QC report for each extraction set by double-clicking the QC Report link in the Summary Report tab. Determine whether the grid has been properly placed by inspec"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Kyonoshin Maruyama"],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling of DJ123 and Nipponbare rice varieties to low-sulfate soil","description":"We conducted an oligo microarray analysis to investigate the gene transcripts in the roots of NB and DJ123 grown in LS and control soils.","dates":{"release":"2026-07-23T00:00:00Z","modification":"2026-07-23T01:00:54.627Z","creation":"2026-03-30T22:15:56.548Z"},"accession":"E-MTAB-13217","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0003789","EFO_0005518","EFO_0003815"]}}