Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MetaboLights MTBLS120 - GNPS Metabolomic Discrimination of Near Isogenic Low and High Phytate Soybean Seeds

ABSTRACT: This data set is downloaded from MetaboLights (http://www.ebi.ac.uk/metabolights/) accession number MTBLS120 Abstract:Methodologies for untargeted metabolomic profiling using liquid chromatography-mass spectrometry (LC-MS) were developed and applied to lipid-depleted methanolic extracts of soybeans seeds obtained from four near isogenic soybean lines (NILs) that differed in phytate content. The four lines differed in mutations for genes encoding two highly homologous multi-drug resistant proteins (MRPs). The double mutant exhibited the low phytate/emergence phenotype whereas the other three NILs, namely the two single mutants and the wild type, did not. Lipid-depleted aqueous methanol extracts were analyzed by orthogonal chromatographic separations (reversed-phase and hydrophilic interaction) in both positive and negative ionization modes. Principal component analysis (PCA) of the LC-MS data clearly separated the low phytate line from the other three, with the major metabolite differences residing in the soyasaponin composition. Group A soyasaponins containing C22-terminated acetylated glucosides were of much lower concentration in the low phytate line, which favored terminally acetylated xyloside-based soyasaponins (soyasaponin A4, A5 and A6). Differing levels of the allergen Gly m 1 were also detected.

INSTRUMENT(S): Synapt G2-S pos

ORGANISM(S): Glycine Max

SUBMITTER: Helm

PROVIDER: MSV000080927 | GNPS | Fri Apr 14 12:43:00 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 Discrimination of Near Isogenic Low and High Phytate Soybean Seeds

Project description:Methodologies for untargeted metabolomic profiling using liquid chromatography-mass spectrometry (LC-MS) were developed and applied to lipid-depleted methanolic extracts of soybeans seeds obtained from four near isogenic soybean lines (NILs) that differed in phytate content. The four lines differed in mutations for genes encoding two highly homologous multi-drug resistant proteins (MRPs). The double mutant exhibited the low phytate/emergence phenotype whereas the other three NILs, namely the two single mutants and the wild type, did not. Lipid-depleted aqueous methanol extracts were analyzed by orthogonal chromatographic separations (reversed-phase and hydrophilic interaction) in both positive and negative ionization modes. Principal component analysis (PCA) of the LC-MS data clearly separated the low phytate line from the other three, with the major metabolite differences residing in the soyasaponin composition. Group A soyasaponins containing C22-terminated acetylated glucosides were of much lower concentration in the low phytate line, which favored terminally acetylated xyloside-based soyasaponins (soyasaponin A4, A5 and A6). Differing levels of the allergen Gly m 1 were also detected.

2016-02-04 | MTBLS120 | MetaboLights

Gene regulation by full length human adiponectin

Project description:Transcriptionnal profiling of 4 human cell lines treated during 3 hours with human adiponectin Keywords: transcriptionnal analysis Four human cell lines (Hela, HepG2, Panc-1, Hek293) were grown until confluence. These cell lines were serum depleted during 2 hours and then treated with human adiponectin (2,5 µg/ml) during 3 hours. Each adiponectin stimulated cell line was compared to depleted cell line. Depleted cell line was considered as control.

2010-12-09 | E-GEOD-14070 | biostudies-arrayexpress

Multi-acetylated histones are a source of carbon for lipid synthesis

Project description:Histone modifications commonly integrate environmental stimuli to cellular metabolic outputs by affecting gene expression. Many modifications, including some histone acetylation marks, do not always correlate to transcription, thus pointing towards an alternative role of histone modifications as potential metabolic reservoirs. Using an approach that integrates mass spectrometry- based epi-proteomics and metabolomics with stable isotope tracer studies, we demonstrate that elevated lipids in histone acetyltransferase (HAT)-depleted hepatocytes result from carbon atoms flowing from the deacetylation of multi-acetylated histone H4 to fatty acids. Consistent with this, the enhanced lipid synthesis in HAT-depleted hepatocytes is dependent on the activity of histone deacetylases (HDACs) and acetyl-CoA synthetase ACSS2. Furthermore, we show that during diet-induced lipid synthesis there is a reduction of multi-acetylated histone H4 in hepatocytes and in mouse liver. In addition, overexpression of histone acetyltransferases can reverse diet-induced lipogenesis by blocking lipid droplet accumulation and maintaining the levels of multi-acetylated histone H4. This study unveils an additional link between epigenetics and metabolism whereby histone acetylation reservoirs may serve as a carbon source for lipid synthesis.

2024-02-14 | PXD042624 | Pride

Comparison of gene expression profiles in chromate transformed BEAS-2B cells

Project description:We established chromate transformed cell lines by chronic exposure of normal human bronchial epithelial BEAS-2B cells to low doses of hexavalent chromium followed by anchorage-independent growth. The gene expression profiles were analyzed in the established cell lines. The gene expression profiles from six chromate transformed cell lines were remarkably similar to each other yet differed significantly from that of either control cell line or normal Beas-2B cells. A total of 409 differentially expressed genes were identified in chromate transformed cells compared to control cells. We analyzed gene expression profiles from 10 cell lines ( six chromated transformed cells lines, three control cell lines, and parental BEAS-2B cells) using Affymetrix Human Gene 1.0 ST array. No techinical replicates were performed.

2010-09-14 | E-GEOD-24025 | biostudies-arrayexpress

Comparison of gene expression profiles in chromate transformed BEAS-2B cells

2010-09-14 | GSE24025 | GEO

Mouse Endothelial Progenitor Cell (EPC) Lines - Illumnia Array

Project description:Mouse EPCs were harvested from lung tissue and cultured in hypoxic chambers (2% FiO2) for 48 hrs and then transferred to regular incubators. Cell lines were then stained for the uptake of the acetylated form of low density lipoprotein. These cells were then sorted by flow cytometry and labeled as EPC_acLDL cells. Finally, high passage EPC_acLDL cells (p16-20) were collected and labeled as EPC_late cells. The three cell lines were then grown up, harvested, and RNA isolated and submitted in duplicate for Illumina array analysis of gene expression.

2013-12-30 | GSE53681 | GEO

Identification and functional analysis of 9p24 amplified genes in human breast cancer

Project description:For the purpose of characterization of the 9p24 amplicon, we carried out high-resolution array CGH (Agilent 244K chip) analysis of four cancer cell lines, including three breast cancer cell lines, Colo824, HCC1954 and HCC70, and one esophageal cancer cell line, KYSE150.

2011-04-29 | GSE28989 | GEO

Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora

Project description:This research investigates the molecular mechanisms of trait deterioration of two experimental lines of entamopathogenic nematodes, an inbred line (L5M) and its original parental line (OHB), created by sub-culturing different experimental lines of the nematode-bacterium complex over 20 passages in insect hosts. These lines differed in their virulence, heat tolerance and fecundity . Transcriptional profiles of the two experimental lines were determined and select differentially expressed genes were validated by quantitative PCR. Samples from four biological replicates each of the parental strain (OHB) and the laboratory strain (L5M) were hybridized to the custom H. bacteriophora arrays.

2010-06-01 | E-GEOD-19152 | biostudies-arrayexpress

Comprehensive expression analyses of neural cell type-specific miRNAs identify new determinants of the specification and maintenance of neuronal phenotypes.

Project description:We performed microarray profiling of miRNA expression across the four principal cell types of the central nervous system: neurons, astrocytes, oligodendrocytes and microglia, isolated from rat cortex. Our microarray results showed that the four cell types differ extensively in their miRNA expression. Over one third of the 351 miRNAs examined had higher than 5-fold differences in expression between two of the four cell types. As expected, cell types of common developmental origin differed least in their miRNA expression profiles (astrocytes and oligodendrocytes), while neurons and microglia showed more unique miRNA expression profiles. 63 miRNAs showed cell type specific enrichment (39 miRNAs) or depletion (24 miRNAs) when comparing the four cell types using criteria of a minimum 5-fold difference in expression in one cell type compared to the average expression in the other three and minimum 2-fold change compared to each of the other three types individually and a false positive rate (FDR) p value lower than 0.01. When comparing only neurons, astrocytes and oligodendrocytes 115 miRNAs were specifically enriched (89 miRNAs) or depleted (36 miRNAs) in one cell type.

2013-06-01 | GSE34614 | GEO

Identifying pH independent hypoxia induced genes in human squamous cell carcinomas in vitro

Project description:Background: Genes upregulated by low oxygen have been suggested as endogenous markers for tumor hypoxia. Yet, most of the genes investigated have shown inconsistent results, which have led to concerns about their ability to be true hypoxia markers. Previous studies have demonstrated that expression of hypoxia induced genes can be affected by extracellular pH (pH e ). Methods: Five different human cell lines (SiHa, FaDu DD, UTSCC5, UTSCC14 and UTSCC15) were exposed to different oxygen concentrations and pH (7.5 or 6.3), and gene expression analyzed with microarray (Affymetrix - Human Genome U133 Plus 2.0 Array). Results: An analysis of two of the cell lines using SAM identified 461 probesets that were able to separate the four groups “ Normal oxygen, normal pH ” , “ Low oxygen, normal pH ” , “ Normal oxygen, low pH ” and “ Low oxygen, low pH ” . From here it was possible to identify a fraction of probesets induced at low oxygen independent of pH in these two cell lines, this fraction included HIG2, NDRG1, PAI1 and RORA. Further verifi cation by qPCR highlighted the necessity of using more cell lines to obtain a robust gene expression profi les. To specifi cally select pH independent hypoxia regulated genes across more cell lines, data for FaDu DD, UTSCC5, UTSCC14 and UTSCC15 were analyzed to identify genes that were induced by hypoxia in each cell line, where the induction was not affected by low pH, and where the gene was not signifi cantly induced by low pH alone. Each cell line had 65 – 122 probesets meeting these criteria. For genes to be considered as target genes (hypoxia inducible pH independent), genes had to be present in three of four cell lines. Conclusion: The result is a robust hypoxia profile unaffected by pH across cell lines consisting of 27 genes. This study demonstrates a way to identify hypoxia markers by microarray, where other factors in the tumor microenvironment are taken into account.

2015-06-20 | GSE70051 | 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