Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS_Bile_acid_modification_fecal_samples_and_synthetic standards of polyamine amidates

ABSTRACT: Mouse and carnivore animal fecal samples obtained from Chris Turck (original dataset: MSV000080574) and Itzik Mizrahi (original dataset: MSV000086131). We recollected untargeted LC-MS/MS on these samples on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Two different chromatographic separation were performed on a Kinetex 2.6 um 100 A pore size C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA). Extracted fecal samples were also spiked with synthetic standards of polyamine bile acid amidates (in different concentrations) to perform retention time matching.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus <mouse, Genus> (ncbitaxon:10088) Mammalia (ncbitaxon:40674)

SUBMITTER: Pieter C Dorrestein

PROVIDER: MSV000091663 | GNPS | Sat Apr 08 00:35:00 BST 2023

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Similar Datasets

Whole-genome sequencing of polyamine over-producing yeast strains

Project description:Dataset aims to uncover beneficial mutations on yeast strains (CEN.PK 113-11D based) engineered for polyamine over-production. We observed substantial heterogeneity between colony sizes and polyamine titers obtained between parent and final strains. Further physiological characterization of re-streaked colonies confirmed this phenotype, meaning that the sudden heterogeneity is heritable. Sequencing data presented here is used for identification differences between these mutated and parental strains.

2021-03-31 | E-MTAB-9898 | biostudies-arrayexpress

Human placenta polyamine

Project description:Polyamine metabolism in the human placenta

| PRJEB45391 | ENA

Temporal transcriptional profiling of polyamine-depleted NIH3T3 cells

Project description:Polyamines are absolutely required for cell growth and proliferation. While polyamine depletion results in reversible cell cycle arrest, the actual mechanism of growth inhibition is still obscure. This work aimed at determining the cellular processes affected by reduction in the intracellular polyamine levels In order to reveal the general transcriptional responses to polyamine depletion in mammalian cells, NIH3T3 mouse fibroblasts were treated with 1mM L-Difluoromethylornithine (DFMO), G1 cellular fractions were collected by sorting at 0,12, 24, 48 and 96 hours upon addition of the reagent, total RNA was extracted, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix MoGene 1.0 ST DNA array.

2012-09-11 | E-GEOD-36445 | biostudies-arrayexpress

Temporal transcriptional profiling of growth resumption following polyamine-depletion

Project description:Polyamines are absolutely required for cell growth and proliferation. While polyamine depletion results in reversible cell cycle arrest, the actual mechanism of growth inhibition is still obscure. This experiment aimed at determining the cellular processes elicited by re-addition of polyamines to polyamine-depleted (growth arrested) cells. In order to reveal the general transcriptional responses to polyamine re-addition, NIH3T3 mouse fibroblasts were first treated with 1mM L-Difluoromethylornithine (DFMO) for 96 hours and then growth stimulated by spermidine. Cells were collected at 0, 30, 60, 120, 240, 360, 480 and 600 min upon addition of spermidine to polyamine-depleted (growth arrested) cells. Total RNA was isolated, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix MoGene 1.0 ST DNA array.

2012-09-11 | E-GEOD-36664 | biostudies-arrayexpress

Temporal transcriptional profiling of polyamine-depleted NIH3T3 cells

2012-09-11 | GSE36445 | GEO

Polyamine biosynthesis in Salmonella

Project description:Verification of the polyamine biosynthesis mutant

| PRJEB35646 | ENA

Temporal transcriptional profiling of growth resumption following polyamine-depletion

2012-09-11 | GSE36664 | GEO

Impact of impaired polyamine biosynthesis on Streptococcus pneumoniae TIGR4 gene expression

Project description:The polyamine biosynthesis gene, speE, in Streptococcus pneumoniae TIGR4 is necessary for survival in murine models of pneumococcal pneumonia. To date, there is no description of polyamine biosynthesis dependent pneumococcal gene expression. In this study, we compared gene expression between the wild-type and biosynthesis deficient (speE) TIGR4 by RNA-Seq analysis.

2023-01-01 | E-MTAB-6070 | biostudies-arrayexpress

Polyamine synthesis effects capsule expression in Streptococcus pneumoniae TIGR4

Project description:Purpose: We recently reported that isogenic deletion of lysine decarboxylase (ΔcadA/SP_0916), an enzyme that catalyzes the biosynthesis of polyamine cadaverine in Streptococcus pneumoniae TIGR4 results in loss of capsular polysaccharide (CPS), which constitutes a novel mechanism of regulation of CPS. Here, we conducted RNA-Seq to elucidate molecular mechanisms of CPS regulation in polyamine synthesis impaired pneumococci. Result: Significantly differentially expressed genes in ΔcadA represent pneumococcal pathways involved in the biosynthesis of precursors for CPS and peptidoglycan. Conclusion: We establish a possible link and interchange between two cellular processes such as high energy demanding capsule production and oxidative stress responses in polyamine synthesis impaired pneumococci (ΔcadA).

2019-09-30 | GSE130511 | GEO

YAP/TAZ drives cell proliferation and tumour growth via a polyamine-eIF5A hypusination-LSD1 axis

Project description:Here using mouse genetic models and human cancer cells, we show that YAP/TAZ reprogram polyamine metabolism to promote cell proliferation and tumor growth. Mechanistically, YAP/TAZ increases polyamine synthesis mainly through direct upregulation of the major rate-limiting enzyme ornithine decarboxylase 1. We further demonstrate that the polyamine spermidine sustains eukaryotic translation factor 5A (eIF5A) hypusination to support efficient translation of histone demethylase LSD1 that maintains a favored epigenetic status for YAP/TAZ-induced cell proliferation. Furthermore, inhibiting either polyamine synthesis or LSD1 can suppress YAP/TAZ-induced cell proliferation in mouse liver and human cancer cells. Thus our study identifies a YAP/TAZ-polyamine-eIF5A hypusination-LSD1 axis as required for YAP/TAZ-induced cell proliferation and tumor growth and suggests LSD1 as a critical target of polyamine in tumorigenesis.

2022-01-01 | GSE174041 | GEO

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