{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Matteo Buti"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13532"],"description":["To get further insights on the micro-nanoplastic (MNP) effects on plants, the aim of this study was to: 1) shed light on the transcriptome changes provoked by two different polyethylene terephthalate (PET) MNPs in plant roots; 2) determine their effects on key plant growth parameters in hydroponically-cultivated Arabidopsis thaliana. MNPs of transparent (Tr-PET) and blue (Bl-PET) material caused a significant reduction in root length, while only Bl-PET significantly reduced rosette area. Plant fresh and dry weight did not change, even though various OJIP-test parameters decreased in the presence of MNPs. RNA-seq data showed that Bl-PET and, especially, Tr-PET affected gene expression in comparison to controls. Tr-PET induced starch degradation and isoprenoids, while glycolysis, trehalose metabolism and fermentation were generally repressed. Tr-PET upregulated genes involved in signaling of xenobiotics, whereas Bl-PET scarcely affected root transcriptomic profile, activating few gene categories for abiotic stresses. Regarding hormones, genes involved in ABA response were repressed, while brassinosteroid-related genes were differentially regulated by Tr-PET. Both MNPs, but especially Tr-PET, upregulated major latex protein-related genes. These results allowed to gain insight into the effects of MNP contamination in plant metabolism, identifying targets for biotechnological strategies to enhance plant tolerance and phytoremediation of these xenobiotic agents."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - 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.).","Library Construction - 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).","Sequencing - RNA-sequencing was performed using Novaseq 6000 SP Reagent Kit (100 cycles). Samples were run in a single flow cell.","Growth Protocol - 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.","Sample Collection - 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.","Sample Treatment - 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The raw reads quality of the six RNA-Seq libraries was assessed using FastQC v0.11.9 2, while adaptors sequences and low quality bases were removed using Trimmomatic v0.39 3 with these parameters: HEADCROP:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:18 MINLEN:40. The filtered RNA reads were aligned to Arabidopsis thaliana TAIR 10 genome assembly using HiSat2 v2.2.1 (Kim et al., 2019). Reads counts were generated from alignment files using featureCounts v1.6.0 software with default parameters, according to ‘exon’ feature and ‘gene_id’ meta-feature of Araport11 annotation file retrieved from Ensembl Plants website","Data Transformation - The EdgeR package was used to filter out unexpressed or poorly expressed genes (a gene was considered to be ‘active’ if the reads per million mapping to that gene were >1 in at least two libraries), and to normalize the RNA libraries depending on their dimension and assigning a CPM value for each active transcript and for each RNA library."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Arabidopsis thaliana"],"pubmed_authors":["Matteo Buti"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic responses to transparent and blue PET micro-nanoplastics in Arabidopsis thaliana","description":"To get further insights on the micro-nanoplastic (MNP) effects on plants, the aim of this study was to: 1) shed light on the transcriptome changes provoked by two different polyethylene terephthalate (PET) MNPs in plant roots; 2) determine their effects on key plant growth parameters in hydroponically-cultivated Arabidopsis thaliana. MNPs of transparent (Tr-PET) and blue (Bl-PET) material caused a significant reduction in root length, while only Bl-PET significantly reduced rosette area. Plant fresh and dry weight did not change, even though various OJIP-test parameters decreased in the presence of MNPs. RNA-seq data showed that Bl-PET and, especially, Tr-PET affected gene expression in comparison to controls. Tr-PET induced starch degradation and isoprenoids, while glycolysis, trehalose metabolism and fermentation were generally repressed. Tr-PET upregulated genes involved in signaling of xenobiotics, whereas Bl-PET scarcely affected root transcriptomic profile, activating few gene categories for abiotic stresses. Regarding hormones, genes involved in ABA response were repressed, while brassinosteroid-related genes were differentially regulated by Tr-PET. Both MNPs, but especially Tr-PET, upregulated major latex protein-related genes. These results allowed to gain insight into the effects of MNP contamination in plant metabolism, identifying targets for biotechnological strategies to enhance plant tolerance and phytoremediation of these xenobiotic agents.","dates":{"release":"2024-12-31T00:00:00Z","modification":"2024-12-22T07:00:21.877Z","creation":"2023-11-16T19:03:06.619Z"},"accession":"E-MTAB-13532","cross_references":{"ENA":["ERP154460"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}