Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DIA-based Proteomics of Rice (Oryza sativa L.) Roots Exposed to Varying polyethylene terephthalate (PET) microplastic Concentrations

ABSTRACT: This project investigates the proteomic responses of rice (Oryza sativa L.) roots subjected to different concentrations of polyethylene terephthalate (PET) microplastic under hydroponic conditions. Data-Independent Acquisition (DIA) was used for proteome acquisition, and MaxQuant was employed for protein identification and quantification. The dataset includes raw mass spectrometry files and associated MaxQuant output tables.

ORGANISM(S): Oryza Sativa

SUBMITTER: Yi Li

PROVIDER: PXD066634 | iProX | Sat Jul 26 00:00:00 BST 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Cold stress and recovery in shoots and roots of Oryza sativa

Project description:Proteomics analyses of roots and shoots of O. sativa plants exposed to cold stress.

2022-02-16 | PXD028712 | Pride

Comparative transcriptomic analysis of iron deficiency response in roots of Oryza sativa and O. rufipogon

Project description:Iron (Fe) is an essential micronutrient for almost all organisms. However, Fe is frequently inaccessible to plants. To acquire insoluble Fe from soil, rice (Oryza sativa L.) plants employ a Combined Strategy, which is composed by all features of Strategy II, common to all Poaceae species, and some features of the Strategy I from non-Poaceae. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in two species from the Oryza genus: O. sativa and its wild progenitor O. rufipogon. A total of 622 and 2,017 genes were found to be differentially expressed in O. sativa and O. rufipogon, respectively. Among the genes regulated in both species, we found the Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2.

2019-11-19 | GSE131238 | GEO

Transcription profiling by array of alfafa seedlings exposed to Arsenic (V)

Project description:After 24 hours of germination, Medicago sativa seedlings were grown with MS nutrient solution and 0, 50, 100 and and 200 microM Na2HAsO4 in a hydroponic system, for 24 hours. Roots were harvest for mRNA extraction and transcritpional analysis.

2015-07-31 | E-MTAB-2158 | biostudies-arrayexpress

Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid.

Project description:BACKGROUND: Autotoxicity plays an important role in regulating crop yield and quality. To help characterize the autotoxicity mechanism of rice, we performed a large-scale, transcriptomic analysis of the rice root response to ferulic acid, an autotoxin from rice straw. RESULTS: Root growth rate was decreased and reactive oxygen species, calcium content and lipoxygenase activity were increased with increasing ferulic acid concentration in roots. Transcriptome analysis revealed more transcripts responsive to short ferulic-acid exposure (1- and 3-h treatments, 1,204 genes) than long exposure (24 h, 176 genes). Induced genes were involved in cell wall formation, chemical detoxification, secondary metabolism, signal transduction, and abiotic stress response. Genes associated with signaling and biosynthesis for ethylene and jasmonic acid were upregulated with ferulic acid. Ferulic acid upregulated ATP-binding cassette and amino acid/auxin permease transporters as well as genes encoding signaling components such as leucine-rich repeat VIII and receptor-like cytoplasmic kinases VII protein kinases, APETALA2/ethylene response factor, WRKY, MYB and Zinc-finger protein expressed in inflorescence meristem transcription factors. CONCLUSIONS: The results of a transcriptome analysis suggest the molecular mechanisms of plants in response to FA, including toxicity, detoxicification and signaling machinery. FA may have a significant effect on inhibiting rice root elongation through modulating ET and JA hormone homeostasis. FA-induced gene expression of AAAP transporters may contribute to detoxicification of the autotoxin. Moreover, the WRKY and Myb TFs and LRR-VIII and SD-2b kinases might regulate downstream genes under FA stress but not general allelochemical stress. This comprehensive description of gene expression information could greatly facilitate our understanding of the mechanisms of autotoxicity in plants.

| S-EPMC4008027 | biostudies-literature

Diversity of cationic antimicrobial peptides in black cumin (Nigella sativa L.) seeds

Project description:Black cumin (Nigella sativa L.) is known to possess a wide variety of antimicrobial peptides belonging to different structural families. Three novel antimicrobial peptides have been isolated from black cumin seeds. Two of them were attributed as members of the non-specific lipid transfer proteins family and one - as a defensin. We have made an attempt of using proteomic approach for novel antimicrobial peptides search in N. sativa seeds as well. The use of well established approach that includes extraction and fractionation stages remains relevant even in case of novel peptides search because the lacking of N. sativa genome data. Novel peptides demonstrate a spectrum of antimicrobial activity against plant pathogenic organisms that may cause economically important crop diseases. These results obtained allow considering these molecules as candidates to be applied in "next-generation" biopesticides development for agriculture use.

2023-07-20 | PXD040611 | Pride

Dynamic Profiles of transcriptome in Oryza sativa leaf

Project description:To evaluate the roles of gene regulation in Oryza sativa leaf, dynamic profiles of transcriptome were investigated in Oryza sativa L. spp. indica with different treatments, the aerial tissues of one-month-old plants from four different areas (groups 1–4) were treated with 0, 40 mL of 25% azoxystrobin, 0.01 g of VdAL, or 40 mL of 25% azoxystrobin plus 0.01 g VdAL, respectively.

2018-12-18 | GSE108204 | GEO

short term abiotic stress Cabernet Sauvignon

Project description:Cabernet Sauvignon plants grown in a hydroponic drip system were treat with 120 mM salt (10:1 NaCl:CaCl), Polyethylene Glycol, cold (5 C) or unstressed. Shoots with leaves were collected at 0, 1, 4, and 8 hours for all treatments, and at 24 hours for all except cold. ****[PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Elizabeth Tattersall. The equivalent experiment is VV1 at PLEXdb.]

2011-08-23 | GSE31594 | GEO

Silicon effect on suberization and lignification in roots of rice (Oryza sativa)

Project description:This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis. 14 days old rice seedlings (Oryza sativa, cv. Selenio) were cultivated for 28 days in non-aerated nutrient solution (mM: 1.43 NH4NO3, 0.32 NaH2PO4 x H2O, 0.51 K2SO4, 1 CaCl2 x 2 H2O, 1.6 MgSO4 x 7 H2O; µM: 1.82 MnSO4, 0.03 (NH4)6Mo7O24, 9 H3BO3, 0.3 ZnSO4 x 7 H2O and 0.15 CuSO4). The pH-value was adjusted to 6.0 by addition of 10 % (v/v) H2SO4 and 0.75 M KOH.Plants were supplied with Si in form of K2SiO3 at concentrations 0 ppm Si (control) and 50 ppm Si (1.78 mM) and potassium in the control treatment was balanced with K2SO4 supply. The plants were grown in a growth chamber (photoperiod: 14 h light, 10 h dark; temperature 25°C day / 20°C night; relative humidity 75 %; light intensity 220 µmol m2 s-1). Adventitious roots were harvested at 0-2 cm and 4-6 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer. To examine transcription of genes related to suberin and lignin synthesis, a self developed microarray containing amongst others ABC transporter, aclytransferases, ß-ketoacyl-CoA synthases and peroxidases was used .

2010-10-10 | GSE23723 | GEO

Gene expression in rice roots in response to inoculation with rice blast fungus

Project description:Rice roots grown in hydroponic culture were inoculated with rice blast fungus and gene expression profiles were analyzed by microarray

2015-04-01 | GSE62895 | GEO

RNA-Seq of water-stressed shoot and root transcriptomes of the emerging biomass and bioenergy species Arundo donax L.

Project description:This study reports the first water-stressed transcriptome of Arundo donax L. (giant reed), a wild species that is emerging as one of the most promising biomass/bionergy species in mediterranean climates. Synchronized cohorts of giant reads cutting grown in hydroponic culture were subjected to water stress by addition of 10% or 20% polyethylene glycol to the roots. Shoot and root amples were collected one hour after stress. Untreated controls were collected at the same time point for shoot and root.

2016-02-19 | E-MTAB-3769 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data