characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-07-18T00:19:55Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-07-18T00:19:55Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113611466
characteristics.characteristic: External Id
characteristics.text: Aquaporins Group. Plant Nutrition Department, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC)
characteristics.characteristic: INSDC center name
characteristics.text: 2023-07-18T00:19:55Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-07-18T00:19:55Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15605645
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13076:B_leaf_1_2
characteristics.characteristic: Submitter Id
characteristics.text: 3
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: naxos
characteristics.characteristic: cultivar
characteristics.text: Protocols: Samples of control and blindness-affected plants were collected from both roots and leaves and ground to a powder using liquid nitrogen. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Total RNA was extracted using the NZY Total RNA Isolation kit (Nzytech, Lisbon, Portugal). Due to the low cell density, after crushing the sample with liquid nitrogen, a total of 500 μl of the resulting pulp was processed by vortexing 20 seconds and subsequently centrifuged (13500 x g, 2 minutes), to separate nucleic acids from cellular material, passing the resultant of this to the first kit column. The rest of process was similar to manufacturer’s protocol. The quantity and purity of RNA was measured with a Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific, USA) and the integrity of the RNA was checked by electrophoresis in agarose gel. Contaminating DNA was removed using RNase for NZY Total RNA Isolation kit (Nzytech, Lisbon, Portugal)according to the manufacturer’s instructions. RIN analysis was performed for prove the integrity of the 8 samples (Schroeder et al., 2006). The RNA extracted was stored at - 80ºC until use. The RNA was sent to the Novogene company (Cambridgeshire, United Kindom) for subsequent sequencing experiments. There, RNA degradation and contamination was monitored on 1% agarose gels, RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), and RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).
characteristics.characteristic: description
characteristics.text: plant blindness
characteristics.characteristic: disease
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: 1
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Brassica oleracea var. italica
characteristics.characteristic: organism
characteristics.text: Brassica oleracea var. italica
characteristics.characteristic: organism
characteristics.text: leaf
characteristics.characteristic: organism part
characteristics.text: 1
characteristics.characteristic: replicate
characteristics.text: Brassica oleracea var. italica
characteristics.characteristic: scientific_name
characteristics.text: B_leaf_1_2
characteristics.characteristic: title