biostudies-arrayexpressMatteo ButiCapsicum annuumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13087Nanotechnology has the potential to revolutionize agriculture by developing engineered nanomaterials to be used as biostimulants, fertilizers, pesticides or smart sensors. Seed priming may represent an opportunity for nano-enabled plant technology to match economic, agronomic and environmental needs. This study investigates the effects of seed priming mediated by iron oxide magnetic nanoparticles (MNPs) in plants. We performed a multilevel integrated study to understand the basic interactions between MNPs and seeds in pepper (Capsicum annuum). Moreover, phenotypic, physiological and molecular analyses were performed to elucidate the biological impact of MNPs from seed to plant development. Interestingly, our findings show positive effects of MNPs on vegetative growth and a profound impact on pepper gene expression patterns. Indeed, we found 2,204 differentially expressed transcripts in nanoprimed seeds, most of them involved in plant defence mechanisms, potentially establishing a seed memory that might enhance the plant's capacity to counteract diverse forms of stress. In conclusion, this work provides a comprehensive investigation about nanoparticle-seed interactions with interesting implications for agricultural technology.biostudies-arrayexpressSample Collection - RNA extraction was performed on a total of 10 seeds for each experimental condition. Three independent biological replicates were included for each treatment, comparing the control group (seeds in MilliQ water for 24 h) with the treatment group exposed to 100 mg/L MNP for 24 h.Sequencing - A sequencing was then run on Illumina Novaseq6000 platform using Novaseq 6000 S1 Reagent Kit (2 ×100 + 10 + 10 bp parameters).Nucleic Acid Extraction - RNA was extracted from ten seeds using 1 mL of TRIzol extraction buffer (Thermo Fisher Scientific, Wilmington, DE, United States) according to the manufacturer’s protocol. RNA concentration was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, United States). The RNA extracted from each sample was treated with DNaseI (NEB) and purified using specific silica-based method following the manufacturer instruction (Monarch RNA Cleanup kit – NEB). The quality of the processed extracts was assessed using Bioanalyzer 2100 system (Kit RNA 6000 Nano - Agilent Technologies).Sample Treatment - Seeds were incubated with 100 mg/L NP and placed on a rotator at room temperature in the dark for 24 hours. Control seeds were kept in MilliQ water and maintained as treated seeds. After the treatment, seeds were rinsed in distilled water and placed in 10 cm Petri dishes on a filter soaked in 2 ml of distilled water.Library Construction - Libraries were processed according to Illumina mRNA Library Prep kit instructions and a unique dual index combination was used for each sample for barcoding. The concentration and quality of the libraries were evaluated using Qubit 4 Fluorometer (dsDNA High Sensitivity Kit - Invitrogen) and Bioanalyzer 2100 system (HS DNA kit – Agilent Technologies).Growth Protocol - Since pepper seeds were the vegetal material used for the experiment, we didn’t use any growth protocol.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence 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 of the six libraries were mapped to Capsicum annuum CM334 reference genome assembly ASM51225v2 downloaded from the Ensembl Plants website. Reads counts were generated from the alignment files using featureCounts v2.0.3 5 with default parameters basing on ‘exon’ feature and ‘transcript_id’ meta-feature of Pepper Genome Annotation (PGA) gene predictions retrieved from EnsemblPlants 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.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNACapsicum annuumMatteo ButifalseEffects of seed priming mediated by iron oxide magnetic nanoparticles (MNPs) in Capsicum annuumNanotechnology has the potential to revolutionize agriculture by developing engineered nanomaterials to be used as biostimulants, fertilizers, pesticides or smart sensors. Seed priming may represent an opportunity for nano-enabled plant technology to match economic, agronomic and environmental needs. This study investigates the effects of seed priming mediated by iron oxide magnetic nanoparticles (MNPs) in plants. We performed a multilevel integrated study to understand the basic interactions between MNPs and seeds in pepper (Capsicum annuum). Moreover, phenotypic, physiological and molecular analyses were performed to elucidate the biological impact of MNPs from seed to plant development. Interestingly, our findings show positive effects of MNPs on vegetative growth and a profound impact on pepper gene expression patterns. Indeed, we found 2,204 differentially expressed transcripts in nanoprimed seeds, most of them involved in plant defence mechanisms, potentially establishing a seed memory that might enhance the plant's capacity to counteract diverse forms of stress. In conclusion, this work provides a comprehensive investigation about nanoparticle-seed interactions with interesting implications for agricultural technology.2023-11-08T00:00:00Z2023-11-09T13:00:14.61Z2023-06-19T14:43:43.503ZE-MTAB-13087ERP148446EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0003969EFO_0004184