characteristics.text: 2024-12-25
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: The University of Edinburgh
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS22461588
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-14631:Water + 0.5mM SA rep A
characteristics.characteristic: Submitter Id
characteristics.text: 12
characteristics.unit: day
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: thale cress
characteristics.characteristic: common name
characteristics.text: Columbia-0
characteristics.characteristic: cultivar
characteristics.text: Protocols: Seedlings were collected with forceps and blotted dry on tissue paper. Seedlings were placed in safelock 1.5ml eppendorf tubes and immediately frozen in liquid nitrogen before storing at -80 degrees celcius. Seeds were sterilised for 15 min. with 50% bleach, 0.1% triton and thoroughly washed with sterile water. Seeds were stratified at 4 degrees celsius for 2-3 days and then were germinated on vertical standing MS plates. Growth conditions: 16/8 hours light/dark cycle with 120 mol m-2 s-1 light and 22 degrees Celsius. Seedlings were placed in 6-well plates and immersed in 10ml of water or 1mM NHP for 18 hours. Seedlings were then removed, blotted dry with tissue paper, then transferred to another 6 well plate and immersed in 10ml water or 0.5mM SA for 6 hours. 1) Grind tissue very fine in liquid nitrogen. 2) Add 0.5 ml RNA extraction buffer (warmed to ~80ºC) and 0.5 ml phenol:chloroform:isoamylalcohol mixture (25:24:1). Vortex vigorously. 3) Centrifuge max. speed for 5 min. at 4ºC, but do not put samples on ice. 4) Transfer the aqueous phase (upper phase) to a new tube. 5) Add 0.5 ml cold chloroform:isoamylalcohol (24:1) and vortex vigorously. 6) Centrifuge max. speed for 5 min. at 4ºC, but do not put samples on ice. 7) Repeat steps 4, 5, and 6. 8)Transfer the aqueous phase to a new tube on ice and add 1/3 volume of 8 M LiCl. 9) Incubate overnight at 4ºC. 10) Centrifuge max. speed for 15 min. at 4ºC. A small clear pellet of total RNA should be visible. From now on keep tubes on ice at all times. 11) Without disturbing the pellet, very carefully remove the supernatant with a pipette. 12) Wash RNA pellet gently with ice-cold (-20ºC) 0.5 ml of 70% ethanol. Do not resuspend pellet. 13) Centrifuge max. speed for 1 min. at 4ºC to make sure the RNA pellet stays in place.Discard supernatant without disturbing the RNA pellet. 14) Repeat step 13 to remove any remaining 70% ethanol. 15) Dry RNA pellet in the SpeedVac for 1 min. without heating. Do not dry longer than this!!! 16) Add 400 μl ddH2O (autoclaved) and keep on ice for 30-60 min. to rehydrate the RNA pellet. 17) Dissolve the RNA pellet by vigorously pipetting the solution up and down. 18) Add 40 μl NaAc pH5.2 and 1 ml of ice-cold (-20ºC) 96% ethanol. Invert to mix (do not vortex!!!). 19) Incubate at least 60 min. at -20ºC. 20) Centrifuge max. speed for 15 min. at 4ºC. A gel-like pellet of pure RNA should now be visible. 21) Without disturbing the pellet, very carefully remove the supernatant with a pipette. 22) Wash RNA pellet gently with ice-cold (-20ºC) 0.5 ml of 70% ethanol. Do not resuspend pellet!!! 23) Centrifuge max. speed for 1 min. at 4ºC to make sure the RNA pellet stays in place. Discard supernatant without disturbing the RNA pellet. 24) Repeat step 23 to remove any remaining 70% ethanol. 25) Dry RNA pellet in the SpeedVac for 1 min. without heating. Do not dry longer than this! 26) Add 25 μl ddH2O (autoclaved) and let sit on ice for 30 min. to rehydrate the RNA pellet. 27) Resuspend RNA pellet by pipetting up and down. 28) RNA was then purified further using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Buffers & Solutions:RNA extraction buffer (autoclave): 100 mM Tris-HCl, pH 8.0; 100 mM LiCl; 10 mM EDTA; 1% SDS; Phenol:chloroform:isoamyl alcohol (25:24:1); Chloroform:isoamylalcohol (24:1); 8M LiCl (autoclave); 3M NaAC, pH 5.2 (autoclave;)70% Ethanol; 96% Ethanol (pure ethanol) Libraries were constructed by Beijing Genomics Institute (BGI), the protocol of which is proprietary.
characteristics.characteristic: description
characteristics.text: seedling development stage
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: long day length regimen
characteristics.characteristic: growth condition
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Arabidopsis thaliana
characteristics.characteristic: organism
characteristics.text: Arabidopsis thaliana
characteristics.characteristic: organism
characteristics.text: whole plant
characteristics.characteristic: organism part
characteristics.text: Arabidopsis thaliana
characteristics.characteristic: scientific_name
characteristics.text: Water + 0.5mM SA rep A
characteristics.characteristic: title