Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RAW data for untargeted metabolomics of rice shoot and root treated with PPE

ABSTRACT: In this study, shoot and root tissues from two-week-old rice plants, treated with peach peel extract (PPE) or mock solution, were harvested 24 hours post-treatment. Metabolites were extracted using 80% methanol with 0.1% formic acid, followed by sonication, centrifugation, and filtration. The extracts were analyzed using LC-MS on a Q Exactive Orbitrap system. Data were acquired in negative ion mode and processed using MS-DIAL software. Feature detection, deconvolution, and alignment were performed, and metabolites were annotated using public MSP spectral libraries. Quality control included pooled QC samples, solvent blanks, and mock-treated controls. This untargeted approach enabled the identification of metabolic shifts associated with PPE-induced systemic resistance in rice, providing insights into the biochemical pathways activated during defense responses.

INSTRUMENT(S): Thermo Q Exactive HF-X Orbitrap

ORGANISM(S): Oryza Sativa (ncbitaxon:4530)

SUBMITTER: yaseen ahmad

PROVIDER: MSV000099534 | MassIVE | Sun Oct 19 02:28:00 BST 2025

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - RAW data for untargeted metabolomics of rice shoot and root treated with PPE

Project description:In this study, shoot and root tissues from two-week-old rice plants, treated with peach peel extract (PPE) or mock solution, were harvested 24 hours post-treatment. Metabolites were extracted using 80% methanol with 0.1% formic acid, followed by sonication, centrifugation, and filtration. The extracts were analyzed using LC-MS on a Q Exactive Orbitrap system. Data were acquired in negative ion mode and processed using MS-DIAL software. Feature detection, deconvolution, and alignment were performed, and metabolites were annotated using public MSP spectral libraries. Quality control included pooled QC samples, solvent blanks, and mock-treated controls. This untargeted approach enabled the identification of metabolic shifts associated with PPE-induced systemic resistance in rice, providing insights into the biochemical pathways activated during defense responses.

2025-10-19 | MSV000099534 | GNPS

WRKY45-dependent rice genes

Project description:WRKY45-dependent rice genes: Mock- and benzothiadiazole (BTH)-treated wild-type (Nipponbare NB) rice and mock- and BTH-treated WRKY45-knockdown (W45-kd) rice (line #15) were analyzed in four biological replicates at 12 and 24 h after the treatment. Mock- and benzothiadiazole (BTH)-treated wild-type (Nipponbare NB) rice and mock- and BTH-treated WRKY45-knockdown (W45-kd) rice (line #3) were analyzed in four biological replicates at 24 h after the treatment.

2012-12-26 | GSE23733 | GEO

Characterization of Gene Expression in Rice Shoot and Root

Project description:The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. The Phalanx microarray platform is based upon the hybridization of a single labeled sample (derived from RNA), followed by one-channel detection. The intensity of the hybridization signal is used to determine target concentration. In order to validate the technical quality of each probe in our arrays, we carried out 10 independent hybridizations on samples representing two different rice tissues – root and shoot. To examine the gene expression profiles between rice root and shoot development, total RNA extracted from rice root and shoot were processed on the rice OneArray® microarray following the standard protocol using five arrays for each tissue type. Raw expression data from 10 microarrays (e.g. 5 arrays × 2 tissues) were normalized and Pearson’s correlation coefficients were calculated for the data sets of hybridization signal intensities.

2013-09-14 | E-GEOD-50844 | biostudies-arrayexpress

Expression data from shoot bases of rice seedling after gravistimulation

Project description:Upper and lower parts (flanks) of rice (Oryza sativa sp. japonica) shoot bases at 0.5 h and 6 h after gravistimulation was used for expression analysis in control and gravistimulated samples.Targets from biological replicates of both control and gravistimulated samples were generated and expression profiles were determined Affymetrix Rice Genome arrays.

2011-09-02 | GSE31834 | GEO

BTA1 controls tiller angle and shoot gravitropism by regulating auxin transport and signaling in rice

Project description:Tiller angle is a key factor determining rice plant architecture, planting density, light interception, photosynthetic efficiency, disease resistance, and grain yield. The distribution of auxin and shoot gravitropism play important roles in regulating tiller angles of rice. Several tiller angle-associated genes have been cloned. However, the mechanisms underlying tiller angle control are far from clear. In this study, we isolate bta1-1, a mutant with an enlarged tiller angle throughout its life cycle. A detailed analysis reveals that BTA1 has multiple functions because several major agronomic traits, including tiller and panicle number, biomass production, secondary branch number per panicle, panicle weight, grain size, and grain weight, are increased in bta1-1 plants. Moreover, BTA1 is a positive regulator of shoot gravitropism in rice. Shoot responses to gravistimulation are disrupted in bta1-1 under both light and dark conditions. Gene cloning reveals that bta1-1 is a novel mutant allele of LA1. LA1 is able to rescue the tiller angle and shoot gravitropism defects observed in bta1-1. BTA1/LA1 is required to regulate the expression of auxin transporters and signaling factors that control shoot gravitropism and tiller angle. High-throughput mRNA sequencing is performed to elucidate the molecular and cellular functions of BTA1/LA1. The results show that BTA1/LA1 may have multiple functions in regulating nucleosome and chromatin assembly, and protein and DNA interactions. Our results provide new insight into the mechanisms whereby BTA1/LA1 controls shoot gravitropism and tiller angle in rice.

2022-02-19 | GSE126759 | GEO

Characterization of Gene Expression in Rice Shoot and Root

2013-09-14 | GSE50844 | GEO

Gene expression profile of rice shoot in response to nitrogen deficiency condition

Project description:Nitrogen (N) are pivotal element for proper plant growth and development. We performed microarray analysis of rice shoot under nitrogen deficiency (-N) to obtain a global view of gene regulations associated with plant response to -N.

2019-10-06 | GSE73772 | GEO

Gene expression profile of rice shoot in response to macronutrient deficiency

Project description:Macronutrients are pivotal elements for proper plant growth and development. We performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions to obtain a global view of gene regulations associated with plant response to essential nutrients.

2015-08-12 | GSE66935 | GEO

Rice acetate treatment

Project description:Transcriptional profiling of rice shoot or root treated with acetate. Goal was to determine the effects of acetate on changes in gene expression.

2021-03-23 | GSE115825 | GEO

Gene expression profile of rice shoot in response to macronutrient excess conditions

Project description:Macronutrients are pivotal elements for proper plant growth and development. We performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) excess to obtain a global view of gene regulations associated with plant response to essential nutrients.

2019-10-06 | GSE73768 | GEO

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