Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS Metabolomics Workbench ST001642 - GNPS Lipidomics in high-risk subjects for the identification of integrated biomarker signatures of type 1 diabetes

ABSTRACT: We present the lipidome of plasma collected from high-risk type 1 diabetes subjects. The methyl tert-butyl ether (MTBE) method was used for lipid extraction, followed by high performance liquid chromatography (HPLC) tandem mass spectrometry (LC-MS/MS) using a Q Exactive Orbitrap mass spectrometer and an Accela 600 HPLC. Lipid species were identified and quantified by analyzing the raw files in LipidSearch 4.2. Further analysis was conducted using Graphpad Prism and Ingenuity Pathway Analysis (IPA).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens

SUBMITTER: Sanjoy Bhattacharya

PROVIDER: MSV000086878 | GNPS | Mon Feb 15 19:24:00 GMT 2021

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression data from zebrafish (Danio rerio) embryos exposed to methyl tert-butyl ether

2013-09-01 | GSE46371 | GEO

Methylibium petroleiphilum PM1 exposed to the fuel-oxygenates methyl-tert-butyl ether and ethanol

Project description:Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel-oxygenates methyl-tert-butyl ether and ethanol High-density whole genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of TBA to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Based on the expression data, hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, alkane monooxygenase as well as propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The global transcriptome response revealed the link between metabolism of MTBE and aromatic compounds (e.g. benzene, toluene) present in gasoline mixtures. The expression data aids our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment. Keywords: bacterial metabolism

2007-10-20 | GSE9381 | GEO

Expression data from zebrafish (Danio rerio) embryos exposed to methyl tert-butyl ether

Project description:Methyl tert-butyl ether (MTBE) has been shown to target developing vasculature in piscine and mammalian model systems. In the zebrafish, MTBE induces vascular lesions throughout development. These lesions result from exposure to MTBE at an early stage in development (6-somites to Prim-5 stages). During this time period, transcript levels of vegfa, vegfc, and vegfr1 were significantly decreased in embryos exposed to 5 mM MTBE. We performed global gene analysis as an unbiased approach to discover possible modes of action of MTBE vascular toxicity. Embryos were exposed at 3 hours post fertilization (hpf) in triplicate to one of three concentrations of MTBE: 5mM (induces vascular lesions and significantly decreases vegfa), 0.625mM (NOAEL; no observed adverse effect level), and 0.00625mM (100-fold below NOAEL), or to embryo media (control). Samples were collected at 6-somites (~15hpf), 21-somites (~24 hpf), and Prim-5 (~30 hpf) stages of development. Embryos were meticulously staged at exposure and at the time of collection to maintain a homogeneous population. Our experimental design sought to explore the effect of three concentrations MTBE on three different stages of zebrafish embryonic development during the critical period established for the chemical. This time period also corresponds to an important time in the cardiovascular system develop of our model vertebrate.

2013-09-01 | E-GEOD-46371 | biostudies-arrayexpress

Serial-Omics of Equine Urine - Serial-omics characterization of equine urine

Project description:Horse urine is easily collected and contains molecules readily measurable using mass spectrometry that can be used as biomarkers representative of health, disease or drug tampering. This study aimed at analyzing microliter levels of horse urine to purify, identify and quantify proteins, polar metabolites and non-polar lipids. Urine from a healthy 12 year old quarter horse mare on a diet of grass hay and vitamin/mineral supplements with limited pasture access was collected for serial-omics characterization. The urine was treated with methyl tert-butyl ether (MTBE) and methanol to partition into three distinct layers for protein, non-polar lipid and polar metabolite content from a single liquid-liquid extraction and was repeated two times. Each layer was analyzed by high performance liquid chromatography – high resolution tandem mass spectrometry (LC-MS/MS) to obtain protein sequence and relative protein levels as well as identify and quantify small polar metabolites and lipids. The results show 46 urine proteins, many related to normal kidney function, structural and circulatory proteins as well as 474 small polar metabolites but only 10 lipid molecules. Metabolites were mostly related to urea cycle and ammonia recycling as well as amino acid related pathways, plant diet specific molecules, etc. The few lipids represented triglycerides and phospholipids. These data show a complete mass spectrometry based –omics characterization of equine urine from a single 333 uL mid-stream urine aliquot. The data can be used as a baseline for healthy urine composition and analyses can be used to monitor disease progression, health status, monitor drug use, etc.

2018-07-23 | PXD007646 | Pride

06 Chemical-induced gene expression changes in rat liver

Project description:tert-Butyl alcohol-induced gene expression changes in rat liver

2016-09-30 | GSE87141 | GEO

Transcription profiling of wild type and mutant fission yeast exposed to different intensities of H202 and two other oxidants

Project description:We studied transcriptional responses of the fission yeast Schizosaccharomyces pombe to different intensities of H2O2 stress as well as two other oxidants: menadione sodium bisulfite and tert-butyl hydroperoxide. DNA microarrays were used to study the changes in expression profiles and the transcriptional regulation. We compare and contrast global expression and regulation of different intensities of H2O2 stress and different oxidants. The transcriptional response to low doses of H2O2 is very similar to menadione sodium bisulfite and the genes were controlled primarily by the transcription factor Pap1. The transcriptional response to medium and high doses of H2O2 is very similar to tert-butyl hydroperoxide and the genes were mostly regulated by the stress-activated MAP kinase Sty1p and the transcription factor Atf1p. We also compare global regulation of oxidative stress genes in fission and budding yeasts and discuss evolutionary implications.

2007-12-07 | E-MEXP-1083 | biostudies-arrayexpress

Characterisation of monophasic solvent-based tissue extractions for detection of polar metabolites and lipids applying UHPLC-MS clinical metabolic phenotyping assays

Project description:<p>Metabolic phenotyping of tissues uses metabolomics and lipidomics to measure the relative polar and non-polar (lipid) metabolite levels in biological samples. This approach aims to understand disease biochemistry and identify biochemical markers of disease. Sample preparation methods must be reproducible, sensitive (high metabolite and lipid yield), and ideally rapid. We evaluated three biphasic methods for polar and non-polar compound extraction (chloroform/methanol/water; dichloromethane/methanol/water; methyl tert-butyl ether [MTBE]/methanol/water), a monophasic method for polar compound extraction (acetonitrile/methanol/water) and a monophasic method for non-polar compound extraction (isopropanol/water). All methods were applied to sheep heart, kidney, and liver tissue. Polar extracts were analysed by hydrophilic interaction chromatography (HILIC) ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) and non-polar extracts by C18 reversed phase UHPLC-MS. Method reproducibility and yield was assessed using multiple annotated endogenous compounds (putatively and MS/MS annotated). Monophasic methods had the highest yield and high reproducibility for both polar (positive ion: median RSD<18%; negative ion: median RSD<28%) and non-polar (positive and negative ion: median RSD<15%) extractions for heart, kidney, and liver. The polar monophasic method extracted higher levels of lipid than biphasic polar extractions, and these lipids caused minimal detection suppression for other compounds during HILIC UHPLC-MS. The non-polar monophasic method had similar or greater detection responses of all detected lipid classes compared to biphasic methods (including increased phosphatidylinositol, phosphatidylserine and cardiolipin responses). Monophasic methods are quicker and simpler than biphasic methods and therefore most suited for future automation.</p>

2020-09-28 | MTBLS1707 | MetaboLights

MZmine3_Nature_Protocol_Lipids_Dataset

Project description:Sheep brain samples extracted with methyl-tert-butyl (Matyash protocol) and analysed by HILIC-IMS-MS.

2023-04-04 | MSV000091633 | MassIVE

MZmine3_Nature_Protocol_Lipid_Dataset

Project description:Sheep brain samples extracted with methyl-tert-butyl ether (Matyash protocol) and analysed by HILIC-IMS-MS.

2023-04-04 | MSV000091642 | MassIVE

Exploring the response of Kluyveromyces lactis to arsenite and peroxide stress and the role of the transcription factor KlYap8 and KlYap1

Project description:The transcriptional response of K. lactis yeast was investigated following exposure to sodium arsenite (As(III)) and tert-butyl hydroperoxide (t-BOOH). We compared the genome-wide expression profile of Klyap8∆ mutant cells to that of the wild type.

2014-10-06 | GSE55128 | 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