Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Urine Latin Square Spike-In for testing the NMR quantification tool, MetaboQuant

ABSTRACT: To test the quantification performance of MetaboQuant and other NMR quantification tools, a set of eight metabolites were added to replicates of a urine sample in varying concentrations. The metabolites were alanine, creatinine, histidine, betaine, acetate, phosphocreatine, β-hydroxybutyrate (BHBA) and lactate. These were added in concentrations of 6000, 3000, 1500, 750, 375, 188, 94, and 47 micromol/L in a Latin Square design. 2D 1H-13C-HSQC spectra were recorded on a 600 MHz Bruker Avance III spectrometer employing a triple-resonance cryoprobe and z-gradients.

INSTRUMENT(S): Bruker

SUBMITTER: Matthias Klein

PROVIDER: MTBLS25 | MetaboLights | 2013-01-10

REPOSITORIES: MetaboLights

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MTBLS25	Other
	FILES	Other
	a_MTBLS25_urine_latin_square_spike-in_for_testing_metaboquant_metabolite_profiling_NMR_spectroscopy.txt	Txt
	i_Investigation.txt	Txt
	m_MTBLS25_urine_latin_square_spike-in_for_testing_metaboquant_metabolite_profiling_NMR_spectroscopy_v2_maf.tsv	Tabular

Items per page:

1 - 5 of 7

Publications

MetaboQuant: a tool combining individual peak calibration and outlier detection for accurate metabolite quantification in 1D (1)H and (1)H-(13)C HSQC NMR spectra.

Klein Matthias S MS Oefner Peter J PJ Gronwald Wolfram W

BioTechniques 20130501 5

Solution nuclear magnetic resonance (NMR) spectroscopy is widely used to analyze complex mixtures of organic compounds such as biological fluids and tissue extracts. Targeted profiling approaches with reliable compound quantitifcation are hampered, however, by signal overlap and other interferences. Here, we present a tool named MetaboQuant for automated compound quantification from pre-processed 1D and 2D heteronuclear single quantum coherence (HSQC) NMR spectral data and concomitant validation ...[more]

PMID: 23662895

Similar Datasets

Osmotic regulation of hepatic choline metabolism

Project description:Betaine critically contributes to the control of hepatocellular hydration and provides protection of the liver from different kinds of stress. This study investigates to what extent hepatocellular hydration changes affect the expression levels of enzymes involved in the metabolism of betaine and related organic osmolytes by using qRT-PCR gene expression studies in rat hepatoma cells as well as metabolic and gene expression profiling in 5,10 - methylene tetrahydrofolate reductase (MTHFR) deficient primary hepatocytes. The results demonstrate a coordinated regulation of betaine degradation and synthesis under anisoosmotic conditions. Expression of betaine degrading enzymes is downregulated by hyperosmolarity and strongly induced by hypoosmolarity. In contrast, synthesis of glycerophosphocholine from phosphoethanolamine and conversion of choline to betaine are both induced by hyperosmolarity but decreased under hypoosmotic conditions. In addition we evaluated the flux of choline and its derivates in liver and plasma of methylene tetrahydrofolate reductase knockout (Mthfr-/-) mice by tandem mass spectrometry. Analyses of system-wide alterations of osmolyte metabolism with microarray studies revealed expression changes similar to those after hypoosmotic exposure in this betaine depletion model. In conclusion, regulation of betaine synthesis and degradation and concomitant changes in intracellular osmolyte concentrations contribute to long-term adaptation to anisoosmotic exposure of the liver. Expression of 280 genes were analyzed in wild type and mthr-/- mice (n=7) with spotted oligonucleotides.

2013-04-01 | E-GEOD-42275 | biostudies-arrayexpress

The effects of phthalates on S. tropicalis development

Project description:Phthalates are added to polymers in order to increase their flexibility, but leach out of the matrix. Given that these plasticizers are mainly found in water bound to particles, aquatic species are exposed to phthalates. Silurana tropicalis eggs were exposed to high concentrations of three pththalates: dicyclohexyl phthalate (DCHP; 19 mg/L), dimethyl phthalate (DMP; 34 mg/L), and monomethyl phthalate (MMP; 1500 mg/L), along to their respective controls: 0.82% DMSO for DCHP, and water controls for DMP and MMP. The exposure lasted 3 days during embryogenesis. Four pooled of 10 larvae were sampled per treatment and analyzed for gene expression changes using a microarray approach.

2014-07-31 | GSE57675 | GEO

Osmotic regulation of hepatic choline metabolism

2013-04-01 | GSE42275 | GEO

High level efficacy of lufenuron against sea lice (Lepeophtheirus salmonis) linked to rapid impact on moulting processes

Project description:This study investigates the transcriptomic responses of salmon lice (L. salmonis) to five concentrations (30, 300, 700, 1000, and 1500 ppb) of lufenuron (Elanco Animal Health)

2018-04-01 | GSE99880 | GEO

The effects of UVB and the organic osmolyte betaine on rat epidermal keratinocytes in an organotypic culture system

Project description:Betaine (trimethylglycine) is a non-toxic, highly water-soluble organic osmolyte widely used in skin care due to its assumed moisturizing and protective properties, but only few studies have addressed its specific effects in skin. Here, the cellular and molecular targets of betaine were analyzed by genome-wide expression analysis in organotypic cultures of rat epidermal keratinocytes (REK). In this model, we also examined whether betaine modifies the impacts of acute UVB exposure. The expression of several genes relevant to epidermal biology, proliferation/differentiation or malignancy as well as solute transport were verified by independent methods (qRT-PCR, western blotting). The data concerning changes in calcium metabolism after UVB exposure has been published separately (Bart et al., Br. J. Dermatol. 171:376-387, 2014). Organotypic cultures of rat epidermal keratinocytes (REK) were prepared by plating cells on a collagen-coated insert (submerged in medium), lifting the confluent cell layer to the air-liquid interface 3 days after plating. These 3D cultures were divided in four treatment groups with three replicates in each: control, betaine (10 mM), UVB (30 mJ/cm2) and betaine + UVB. Betaine was added to the cultures for 11 days, starting from day 4 until sample collection. UVB exposure was performed 24 h prior to sample collection for 2-week-old 3D cultures with a well-formed epidermal layer. For further details on the experimental set-up and characteristics of the UV source, please refer to Bart et al. (Br. J. Dermatol. 171:376-387, 2014) and Rauhala et al. (J. Biol. Chem. 288:17999-18012, 2013).

2015-10-26 | E-GEOD-63004 | biostudies-arrayexpress

Inhalation exposure of hexanal in rats (mRNA)

Project description:To further development of insight into the mechanism of toxicity, it is important to employ whole genome microarray expression profiling as a discovery platform to ientify genes with the potential to distinguish hexanal exposure across an exposure range relevant for toxicologic mechanisms. However, few reports have described the effect of hexanal on gene expression profiles using animal model. In this respect, we studied the expression profiles of mRNAs in hexanal-exposed in rats by microarray analysis. To evaluate the gene expression in lung tissue of rats after exposure of hexanal, Fischer-344 rats were inhaled to three concentrations (600, 1000, 1500 mg/m3) for 5 weeks. mRNA expression analysis was conducted using Rat GE(v3) 4X44K microarray (Agilent Technologies, USA).

2014-08-06 | E-GEOD-60118 | biostudies-arrayexpress

Inhalation exposure of hexanal in rats (miRNA)

Project description:To further development of insight into the mechanism of toxicity, it is important to employ whole genome microarray expression profiling to identify and characterize miRNAs profiles as a discovery platform relevant for toxicologic mechanisms of hexanal. miRNAs have prominent role in cell cycle control, apoptosis, cancer development and proliferation-related processes. However, few reports have described the effect of hexanal on miRNA expression profiles using animal model. In this respect, we studied the expression profiles of miRNAs in hexanal-exposed in rats by miRNA microarray analysis. To evaluate the miRNA expression in lung tissue of rats after exposure of hexanal, Fischer-344 rats were inhaled to three concentrations (600, 1000, 1500 mg/m3) for 5 weeks. miRNA expression analysis was conducted using Rat miRNA 8 x 15K microarray v19.0 (Agilent Technologies, USA).

2014-08-08 | E-GEOD-60203 | biostudies-arrayexpress

Detection call p-values for Affymetrix low level spike-in experiment

Project description:Four different concentrations (0, 0.75, 1.5, 3 pM) of genes were spiked in groups (group size 6-7 transcripts) Each concentration combination were spiked into a common backgroung sample (HeLa cell line) and hybridized to three HG-U133A Plus 2.0 Arrays. Keywords: Latin square design for HG-U133A Plus 2.0 GeneChips

2009-11-10 | GSE17968 | GEO

Whole blood DNA methylation profiling of glucocorticoid excess

Project description:Evaluation of whole blood DNA methylome in 94 samples obtained from 47 patients with different glucocorticoid states, including Cushing’s syndrome, eucortisolism and adrenal insufficiency, in order to identify a molecular signature reflecting glucocorticoid action.

2022-01-19 | E-MTAB-10092 | biostudies-arrayexpress

Molecular signatures of the Eagle effect induced by the artificial siderophore conjugate LP-600 in E. coli

Project description:We investigated a paradoxical re-growth of E. coli upon treatment of a novel siderophore-conjugate, LP-600, at concentrations 16-32 times above the minimum inhibitory concentration (MIC).Transcriptome analysis revealed that LP-600 induced the expression of genes involved in SOS response and e14 prophage upon regrowth conditions.

2022-07-31 | GSE197880 | 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