Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MetaboLights MTBLS372 - GNPS Metabolomic profiling of Fraxinus excelsior genotypes tolerant or susceptible to ash dieback disease reveals changes in iridoid glycosides

ABSTRACT: This data set is downloaded from MetaboLights (http://www.ebi.ac.uk/metabolights/) accession number MTBLS372 Abstract:European common ash, Fraxinus excelsior L., is currently threatened by Ash dieback (ADB) caused by the fungus, Hymenoscyphus fraxineus. To detect and identify metabolites that may be products of pathways important in contributing to resistance against H. fraxineus we performed untargeted metabolomic profiling on leaves from selected F. excelsior individuals showing strong tolerance or susceptibility to H. fraxineus. We identified sets of “features” [small molecules] that enabled strong discrimination between tolerant or susceptible genotypes of F. excelsior. Strikingly, tolerant F. excelsior lines exhibited low levels of iridoid glycosides, known anti-feeding deterrents. As Europe is threatened by Emerald Ash Borer (Agrilus planipennis), an invasive wood boring beetle native to East Asia that has devastated North American ash, our study raises the question whether selection for resistance to H. fraxineus leads to ecological trade-offs that result in susceptibility to emerging pests such as emerald ash borer.

INSTRUMENT(S): 6520 Q-TOF LC/MS (Agilent)

ORGANISM(S): Fraxinus Excelsior

SUBMITTER: Sambles

PROVIDER: MSV000080960 | GNPS | Mon Apr 17 08:22:00 BST 2017

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Metabolomic profiling of Fraxinus excelsior genotypes tolerant or susceptible to ash dieback disease reveals changes in iridoid glycosides

Project description:European common ash, Fraxinus excelsior L., is currently threatened by Ash dieback (ADB) caused by the fungus, Hymenoscyphus fraxineus. To detect and identify metabolites that may be products of pathways important in contributing to resistance against H. fraxineus we performed untargeted metabolomic profiling on leaves from selected F. excelsior individuals showing strong tolerance or susceptibility to H. fraxineus. We identified sets of "features" [small molecules] that enabled strong discrimination between tolerant or susceptible genotypes of F. excelsior. Strikingly, tolerant F. excelsior lines exhibited low levels of iridoid glycosides, known anti-feeding deterrents. As Europe is threatened by Emerald Ash Borer (Agrilus planipennis), an invasive wood boring beetle native to East Asia that has devastated North American ash, our study raises the question whether selection for resistance to H. fraxineus leads to ecological trade-offs that result in susceptibility to emerging pests such as emerald ash borer.

2016-11-09 | MTBLS372 | MetaboLights

Single-cell transcriptomics of East-Asian pancreatic islets cells

Project description:Single-cell RNA-seq (scRNA-seq) of pancreatic islets have reported on α- and β-cell gene expression in mice and subjects of predominantly European ancestry. We aimed to assess these findings in East-Asian islet-cells. 448 islet-cells were captured from three East-Asian non-diabetic subjects for scRNA-seq. Hierarchical clustering using pancreatic cell lineage genes was used to assign cells into cell-types. Differentially expressed transcripts between α- and β-cells were detected using ANOVA and in silico replications of mouse and human islet cell genes were performed. We identified 118 α, 105 β, 6 δ endocrine cells and 47 exocrine cells. Besides INS and GCG, 26 genes showed differential expression between α- and β-cells. 10 genes showed concordant expression as reported in rodents, while FAM46A was significantly discordant. Comparing our East-Asian data with data from primarily European subjects, we replicated several genes implicated in nuclear receptor activations, acute phase response pathway, glutaryl-CoA/tryptophan degradations and EIF2/AMPK/mTOR signaling. Additionally, we identified protein ubiquitination to be associated among East-Asian β-cells. We report on East-Asian α- and β-cell gene signatures and substantiate several genes/pathways. We identify expression signatures in East-Asian β-cells that perhaps reflects increased susceptibility to cell-death and warrants future validations to fully appreciate their role in East-Asian diabetes pathogenesis.

2017-08-11 | GSE97655 | GEO

The Caucasus as an asymmetric semipermeable barrier to ancient human migrations

Project description:The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.

2012-04-18 | GSE37342 | GEO

The Caucasus as an asymmetric semipermeable barrier to ancient human migrations

2012-04-17 | E-GEOD-37342 | biostudies-arrayexpress

MERLION LUNG CANCER STUDY_2_DNA

Project description:East-Asian (EA) patients with Non Small Cell Lung Cancer (NSCLC) are associated with a high proportion of non-smoking women, EGFR activating somatic mutations, and clinical responses to tyrosine kinase inhibitors. We identify copy number alterations specific to EA and Western European (WE) NSCLCs and conducted an integrative analysis using transcritomic data for identifying copy-number-driven candidate genes. Samples were hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center. 226 lung adenocarcinomas (90 East-Asian and 136 Western-European) were analyzed for copy-number aberrations (CNAs) using a common high resolution SNP microarray platform.

2011-11-22 | E-GEOD-33848 | biostudies-arrayexpress

Gene expression breast cancer

Project description:There exists a common deletion polymorphism on the genetic loci of APOBEC3B and this polymorphism exist in ~37% of East Asians and ~7% of Europeans. Germline APOBEC3B deletion has bee27233495n shown to confer modest risk to breast cancer in both East Asian women and women of European descent We performed expression profiling by array to investigate the significantly differentially expressed genes and enriched gene sets in APOBEC3B-null vs. APOBEC3B breast cancers

2016-09-18 | GSE73540 | GEO

Metabolic and transcriptional response of Arabidopsis thaliana wildtype and mutants to Phytophtora infestans

Project description:The oomycete P. infestans is the causal agent of late blight, the most devastating potato disease. In contrast to potato, A. thaliana is able to successfully prevent colonization of the pathogen due to a multi-layered nonhost resistance. Several mutants have been isolated which are impaired in penetration resistance. A mutation in the gene PEN2, which encodes for an enzyme involved in indole glucosinolate metabolism (Bednarek et al. (2009)), results in the loss of penetration resistance against P. infestans (Lipka et al. (2005)). Despite its ability to penetrate epidermal cells of pen2 mutant plants, P. infestans is still not able to colonize these plants. Additional mutants were isolated by Kopischke et al. (2013) which show enhanced defense responses upon infection with P. infestans: pen2erp1 and pen2erp2, and backcrossed mutants erp140 and erp2D. We used six different plant lines, the wildtype-like gl1, and the five different mutants (pen2, pen2erp1, pen2erp2, erp2D, erp140). The plants were either infected with P. infestans spores or treated with water as control, and harvested 6h and 12h after treatment. The experiment was repeated three times with different P. infestans cultures, resulting in biological triplicates, for an overall of 6 x 2 x 2 x 3 = 72 samples. A metabolomics data set from the same set of samples has been submitted to MetaboLights database at EMBL-EBI (http://www.ebi.ac.uk/metabolights/index) under accession number MTBLS18 .

2019-01-25 | E-MTAB-3287 | biostudies-arrayexpress

A microarrays-based analysis of gametogenesis in two Portuguese populations of the European clam Ruditapes decussatus

Project description:The European clam, Ruditapes decussatus (Linnaeus, 1758) is a bivalve mollusc of the family Veneridae native to the European Atlantic and Mediterranean coastal waters. Its production is exclusively based on natural recruitment, which is subject to high annual fluctuations due to adversely affected by pollution and other environmental factors. Microarray analyses have been performed in four gonadal maturation stages of two higly productive Portuguese wild populations (Ria Formosa in South and Ria de Aveiro in North) characterized by different responses to spawning induction.

2014-06-03 | GSE51150 | GEO