Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Understanding the molecular mechanisms of drought tolerance in wild soybean (Glycine soja) through multi-omics-based alternative splicing predictions

ABSTRACT: This work is managed by Pf Jae Yoon Kim from Kongju National University of South Korea.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Glycine Soja (ncbitaxon:3848)

SUBMITTER: Heeyoun Hwang

PROVIDER: MSV000093913 | GNPS | Wed Jan 24 09:53:00 GMT 2024

SECONDARY ACCESSION(S): PXD048845

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Similar Datasets

Understanding the molecular mechanisms of drought tolerance in wild soybean (Glycine soja) through multi-omics-based alternative splicing predictions

Project description:This work is managed by Pf Jae Yoon Kim from Kongju National University of South Korea.

2024-01-24 | MSV000093913 | MassIVE

Multi-omics analysis reveals molecular mechanisms of shoot adaption to salt stress in Tibetan wild barley.

Project description:Tibetan wild barley (Hordeum spontaneum L.) has been confirmed to contain elite accessions in tolerance to abiotic stresses, including salinity. However, molecular mechanisms underlying genotypic difference of salt tolerance in wild barley are unknown.In this study, two Tibetan wild barley accessions (XZ26 and XZ169), differing greatly in salt tolerance, were used to determine changes of ionomic, metabolomic and proteomic profiles in the shoots exposed to salt stress at seedling stage. Compared with XZ169, XZ26 showed better shoot growth and less Na accumulation after 7 days treatments. Salt stress caused significant reduction in concentrations of sucrose and metabolites involved in glycolysis pathway in XZ169, and elevated level of tricarboxylic acid (TCA) cycle, as reflected by up-accumulation of citric acid, aconitic acid and succinic acid, especially under high salinity, but not in XZ26. Correspondingly, proteomic analysis further proved the findings from the metabolomic study.XZ26 maintained a lower Na concentration in the shoots and developed superior shoot adaptive strategies to salt stress. The current result provides possible utilization of Tibetan wild barley in developing barley cultivars for salt tolerance.

| S-EPMC5100661 | biostudies-literature

Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction.

Project description:In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root-mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with 15 transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.

| S-EPMC4717292 | biostudies-literature

Multi-Omics Revealed Molecular Mechanisms Underlying Guard Cell Systemic Acquired Resistance.

Project description:Systemic Acquired Resistance (SAR) improves immunity of plant systemic tissue after local exposure to a pathogen. Guard cells that form stomatal pores on leaf surfaces recognize bacterial pathogens via pattern recognition receptors, such as Flagellin Sensitive 2 (FLS2). However, how SAR affects stomatal immunity is not known. In this study, we aim to reveal molecular mechanisms underlying the guard cell response to SAR using multi-omics of proteins, metabolites and lipids. Arabidopsis plants previously exposed to pathogenic bacteria Pseudomonas syringae pv. tomato DC3000 (Pst) exhibit an altered stomatal response compared to control plants when they are later exposed to the bacteria. Reduced stomatal apertures of SAR primed plants lead to decreased number of bacteria in leaves. Multi-omics has revealed molecular components of SAR response specific to guard cells functions, including potential roles of reactive oxygen species (ROS) and fatty acid signaling. Our results show an increase in palmitic acid and its derivative in the primed guard cells. Palmitic acid may play a role as an activator of FLS2, which initiates stomatal immune response. Improved understanding of how SAR signals affect stomatal immunity can aid biotechnology and marker-based breeding of crops for enhanced disease resistance.

| S-EPMC7795379 | biostudies-literature

Characterization of altered molecular mechanisms in Parkinson’s disease through cell type-resolved multi-omics analyses

Project description:Parkinson’s disease (PD) is a progressive neurodegenerative disorder. However, cell type-dependent transcriptional regulatory programs responsible for PD pathogenesis remain elusive. Here, we establish transcriptomic and epigenomic landscapes of the substantia nigra (SN) by profiling 113,207 nuclei obtained from healthy controls and PD patients. Our multi-omic data integration provides cell type annotation of 128,724 cis-regulatory elements (cREs), and uncovers cell type-specific dysregulations in cREs with a strong transcriptional influence on genes implicated in PD. The establishment of high-resolution three-dimensional (3D) chromatin contact maps identifies 656 target genes of dysregulated cREs and genetic risk loci, uncovering both potential and known PD risk genes. Notably, these candidate genes exhibit modular gene expression patterns with unique molecular signatures in distinct cell types, highlighting altered molecular mechanisms in dopaminergic neurons and glial cells including oligodendrocytes and microglia. Together, our single-cell transcriptome and epigenome reveal cell type-specific disruption in transcriptional regulations related to PD.

2023-03-05 | GSE148434 | GEO

SNParray data for banking lines in Korea National Stem Cell Bank

Project description:Copy number variantions (CNVs) were calculated using SNP array data for banking lines in Korea National Stem Cell Bank.

2021-01-05 | GSE163134 | GEO

Analysis of gene expression patterns of arabidopsis whitening mutant wn1 and wild-type

Project description:This data analyzes gene expression patterns in Arabidopsis whitening mutants, wn1, with defects in chloroplast development. We found that wn1 was a T-DNA insertion line of Arabidopsis AtPTAC10/PAP3 (At3g48500) and exhibited a lethal, albino-like phenotype in the seedling stages. pTAC10 was known as a component of RNA polymerase complex called plastid-encoded RNA polymerase, PEP, in mature chloroplasts. Because wn1 mutants were lethal, we extracted RNA from cotyledons of 7-day-old seedlings from wn1 mutants and Col-0. RNA seq analysis was commissioned by NICEM in Seoul National University, Korea and transcriptome resequencing was confirmed in Macrogen, Korea. Through analysis, we compared gene expression patterns of wn1 mutant and Col-0 seedlings.

2017-04-02 | GSE90159 | GEO

Agelena koreana whole body and venom gland transcriptome

Project description:Agelena koreana is indigenous spider in South Korea that lives on piles of trees building webs. RNA-sequencing was performed for venom gland tissue and whole body except venom gland.

2022-02-23 | GSE197102 | GEO

GNPS Massive - KoLRI lichen extract (DDA / negative ion mode)

Project description:A LC-MS/MS (Data-dependent acquisition in negative ion mode) dataset from Lichen extracts acquired from Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea.

2021-07-03 | MSV000087749 | GNPS

GNPS - KoLRI lichen extract (DDA / negative ion mode)

2021-07-04 | MSV000087754 | GNPS

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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