characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-01-31T00:19:40Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-01-31T00:19:40Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110295302
characteristics.characteristic: External Id
characteristics.text: PhD student
characteristics.characteristic: INSDC center name
characteristics.text: 2023-01-31T00:19:40Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-01-31T00:19:40Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12392910
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11927:LN3_Roots
characteristics.characteristic: Submitter Id
characteristics.text: 15
characteristics.unit: day
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: bread wheat
characteristics.characteristic: common name
characteristics.text: Graham
characteristics.characteristic: cultivar
characteristics.text: Protocols: The whole root system and the basal node of wheat plants were harvested at different time points depending on the experimental design. Samples were quickly frozen in liquid nitrogen and stored at -80 oC until processing. In this study, the basal node is called the 0.5 cm long section from the base of the main shoot, which includes the shoot apical meristem, lateral buds and leaf meristems. After removing all the roots from the shoot, the outgrown primary tillers were also carefully removed, and 0.5 cm of the main shoot base was dissected. Tissue samples from 3 plants were pooled per biological replicate. Plants were grown hydroponically on top of 5 L black pots containing the nutrient solution under constant aeration. The biostimulant used was a microalgae extract based product specifically formulated for the hydroponic culture, which was added in the nutrient solution. Plants grown in the same pot (3 plants per pot) were considered pseudoreplicates, and they were pooled together to form a biological replicate. The experiment was conducted in a standard glasshouse equipped with high-pressure sodium lights (14 h day length, 20/18 oC day and night temperature, respectively). Total RNA was extracted from approximately 100 mg of frozen tissue using TRIzol reagent (Invitrogen) following the manufacturer's protocol. To ensure no DNA carryover, DNase treatment was performed using RQ1 RNase-Free DNase (Promega). After DNase treatment RNA was further purified by phenol/chloroform/isoamyl-alcohol purification. Extracted total RNA from basal node samples was further purified with Plant RNeasy kit (Qiagen) following the provided RNA clean-up protocol. A modified hot phenol extraction protocol was used for extracting RNA from approximately 500 mg of root tissue (Verwoerd et al., 1989). DNase treatment and further phenol/chloroform/isoamyl-alcohol RNA purification steps were performed as described above. Quality control, poly-A selection for rRNA removal, library preparation, multiplexing were performed by Azenta/Genewiz UK according to their standard workflow. Briefly, RNA library preparation was prepared using NEBNext Ultra II Library Prep Kit for Illumina following the manufacturer's protocol (NEB). Firstly, oligo-dt beads were used for mRNA enrichment, and the mRNAs were fragmented for 15 min at 94 oC. First and second strand cDNA were subsequently synthesized. Indexed adapters were ligated to cDNA fragments after adenylation of the 3' end of the cDNA fragments. Limited cycle PCR was used for library amplification. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies) and quantified by using Qubit 4.0 Fluorometer (Invitrogen) or equivalent.
characteristics.characteristic: description
characteristics.text: leaf production stage
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: low nitrogen
characteristics.characteristic: growth condition
characteristics.text: Triticum aestivum
characteristics.characteristic: organism
characteristics.text: Triticum aestivum
characteristics.characteristic: organism
characteristics.text: root
characteristics.characteristic: organism part
characteristics.text: Triticum aestivum
characteristics.characteristic: scientific_name
characteristics.text: LN3_Roots
characteristics.characteristic: title