characteristics.text: 2024-01-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: SAMEA114622023
characteristics.characteristic: External Id
characteristics.text: University of Florence
characteristics.characteristic: INSDC center name
characteristics.text: 2023-11-15T17:46:02Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS16997407
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13532:NP-21_S45
characteristics.characteristic: Submitter Id
characteristics.text: 34
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: Col-0
characteristics.characteristic: cultivar
characteristics.text: Protocols: At the end of the exposure time, roots were collected from plants grown in control conditions and in the presence of Tr-PET and Bl-PET MNPs. Three biological replicates were considered for each of the three conditions (1 biological replicate = 1 plant). Roots were immediately frozen in liquid nitrogen and stored at − 80 °C. Seeds of A. thaliana Col-0 were stratified for 24 h in the dark at room temperature to promote synchronous germination. The hydroponic growth system developed by Conn et al. (2013), with slight modifications, was used in this experiment because it allows simple handling of small plants without disturbing them. Ten-day-old seedlings were randomly transferred to one of the following treatment conditions: i) control (C), 90 mL half strength Hoagland’s solution prepared in distilled water; ii) 90 mL half strength Hoagland’s solution prepared in Tr-PET solution (Tr-PET); iii) 90 mL half strength Hoagland’s solution prepared in Bl-PET solution (Bl-PET). The different growing solutions were placed inside externally dark-coated cylindric glass vessels (11 cm height, 4 cm base diameter) and 8 vessels per treatment were prepared for a total of 24 replicates; the employed MNP concentrations (around 0.1 g L-1) were comparable to those reported for contaminated freshwaters. Plants were grown for 17 days in a climate chamber with the following controlled conditions: 24/16 °C day/night, light intensity 300 µmol m−2 s −1, 16-h (day) photoperiod and relative humidity 60–65%. The nutrient solutions, with or without MNPs, were vigorously shaken with a glass rod each 2 days to reduce suspension and/or aggregation of the plastic particles. RNA extraction was performed using 100 mg of leaves ground with a pestle and mortar in liquid nitrogen using the RNeasy Plant Mini kit (Qiagen). Final elutions were performed using 60 μL of RNase-free water. RNA quality was determined using the Agilent 2100 Bioanalyzer System (RNA 6000 nano kit - Biorad Inc.). Nine sequencing libraries were obtained following the procedure of Truseq Stranded mRNA Library Prep (Illumina) and using Truseq RNA Single Indexes (3 libraries for each of the three experimental conditions). The concentration of each library was determined using Qubit™ 4 Fluorometer (dsDNA High Sensitivity Kit - Invitrogen).
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: not applicable
characteristics.characteristic: isolate
characteristics.text: Arabidopsis thaliana
characteristics.characteristic: organism
characteristics.text: Arabidopsis thaliana
characteristics.characteristic: organism
characteristics.text: root
characteristics.characteristic: organism part
characteristics.text: Arabidopsis thaliana
characteristics.characteristic: scientific_name
characteristics.text: control
characteristics.characteristic: stimulus
characteristics.text: NP-21_S45
characteristics.characteristic: title