Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Geotraces EPZT

ABSTRACT: Surface seawater ENV solid phase extraction samples collected on the US GEOTRACES EPZT cruise (October-December 2013).

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Environmental Samples <bacillariophyta> (ncbitaxon:33858)

SUBMITTER: Daniel Repeta

PROVIDER: MSV000080173 | MassIVE |

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Publications

Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean.

Boiteau Rene M RM Mende Daniel R DR Hawco Nicholas J NJ McIlvin Matthew R MR Fitzsimmons Jessica N JN Saito Mak A MA Sedwick Peter N PN DeLong Edward F EF Repeta Daniel J DJ

Proceedings of the National Academy of Sciences of the United States of America 20161201 50

Nearly all iron dissolved in the ocean is complexed by strong organic ligands of unknown composition. The effect of ligand composition on microbial iron acquisition is poorly understood, but amendment experiments using model ligands show they can facilitate or impede iron uptake depending on their identity. Here we show that siderophores, organic compounds synthesized by microbes to facilitate iron uptake, are a dynamic component of the marine ligand pool in the eastern tropical Pacific Ocean. S ...[more]

PMID: 27911777

Similar Datasets

Untargeted metabolomics analysis of dissolved organic matter in the western Atlantic Ocean

Project description:<p>The data are dissolved organic compounds from three stations sampled in the western Atlantic Ocean in 2013. Seawater samples spanning from the surface ocean to the seafloor were collected, filtered, acidified, and extracted using solid phase extraction with Bond Elut PPL cartridges. The extracts were separated using reversed phase chromatography and analyzed with ultrahigh resolution mass spectrometry in negative ion mode. The resulting data are features, or a unique combination of mass-to -charge values and retention time. </p>

2024-02-28 | MTBLS6735 | MetaboLights

Chip-SIP analysis of Monterey Bay surface waters incubated with organic carbon substrates

Project description:October 2013 surface seawater collected from Monterey Bay was incubated with 1 micromolar 13C labeled glucose, starch, acetate, lipids, protein, or amino acids for 12 hours. Community RNA was extracted and hybridized to a Roche Nimblegen microarray and analyzed by NanoSIMS to obtain isotope ratio data for all probe spots.

2015-07-23 | GSE71228 | GEO

GNPS - <Surface seawater collected inside and outside a Sargassum patch in the Atlantic Ocean>

Project description:Surface seawater samples collected from the Atlantic Ocean. Three types of samples were collected: seawater inside a patch of Sargassum ('in'), seawater in the downstream slick of Sargassum ('slick'), and seawater outside the patch ('out'). Samples were collected by hand from a small boat, and DOM was extracted using solid phase extraction with Bond Elut PPL cartridges. Both positive and negative ion mode data are available.

2023-11-01 | MSV000093224 | GNPS

Chip-SIP analysis of Monterey Bay surface waters incubated with organic carbon substrates

2015-07-23 | E-GEOD-71228 | biostudies-arrayexpress

GNPS Element-selective targeting of nutrient metabolites in environmental samples by ICPMS and ESIMS

Project description:Seawater and culture ENV solid phase extraction samples

2021-02-27 | MSV000086964 | GNPS

Chip-SIP analysis of Pacifica pier surface waters incubated with organic and inorganic nitrogen and carbon substrates

Project description:October 2010 surface seawater collected from Pacifica pier was incubated with 14 different substrates for 12 hours. Community RNA was extracted and hybridized to a Roche Nimblegen microarray and analyzed by NanoSIMS to obtain isotope ratio data for all probe spots.

2018-03-03 | GSE111361 | GEO

Quantification of Dissolved Metabolites in Environmental Samples through Cation-Exchange Solid Phase Extraction (CX-SPE) paired with Liquid Chromatography-Mass Spectrometry

Project description:Small, biologically produced, organic molecules called metabolites play key roles in microbial systems where they directly mediate exchanges of nutrients, energy, and information. However, the study of dissolved polar metabolites in seawater and other environmental matrices has been hampered by analytical challenges including high inorganic ion concentrations, low analyte concentrations, and high chemical diversity. Here we show that a cation-exchange solid phase extraction (CX-SPE) sample preparation approach separates positively charged and zwitterionic metabolites from seawater and freshwater samples, allowing their analysis by liquid chromatography-mass spectrometry (LC-MS). We successfully extracted 69 known compounds from an in-house compound collection and evaluated the performance of the method by establishing extraction efficiencies and limits of detection (pM to low nM range) for these compounds. CX-SPE extracted a range of compounds including amino acids and compatible solutes, resulted in very low matrix effects, and performed robustly across large variations in salinity and dissolved organic matter (DOM) concentration. We compared CX-SPE to an established solid phase extraction procedure (PPL-SPE) and demonstrate that these two methods extract fundamentally different fractions of the dissolved metabolite pool with CX-SPE extracting compounds that are on average smaller and more polar. We use CX-SPE to analyze four environmental samples from distinct aquatic biomes, producing some of the first CX-SPE dissolved metabolomes. Quantified compounds ranged in concentration from 0.0093 nM to 49 nM and were composed primarily of amino acids (0.15 – 16 nM) and compatible solutes such as TMAO (0.89 – 49 nM) and glycine betaine (2.8 – 5.2 nM).

2022-08-30 | ST002292 | MetabolomicsWorkbench

Comparison of Porphyromonas gingivalis 381 and W83 gene expression between surface translocation and biofilm mode

Project description:Porphyromonas gingivalis (P. gingivalis) 381 and W83 growing in motility condition (i.e. stabbed in soft agar culture) and on surface of solid agar culture (Biofilm) were prepared. Applied medium was BAPHK supplemented with hemin and menadione . The cultures were then permitted to grow anaerobically at 37°C for 24 hours, which corresponds to initial stages of surface translocation by P. gingivalis. At this point, RNA extraction was performed using the cultures, and these samples were processed and submitted for RNA sequencing using an Illumina platform. Significant changes in gene expression were observed in cells growing in motility and biofilm modes , and the majority of changes were associated with cell surface proteins, membrane proteins, biosynthesis of folates and bioenergetic pathways.

2019-03-31 | GSE128025 | GEO

Guselkumab (interleukin-23-specific monoclonal antibody) demonstrates clinical and molecular response in moderate-to-severe psoriasis

Project description:A gene expression profiling study was conducted in which skin biopsy samples were collected for RNA extraction and hybridization to microarrays from patients with moderate-to-severe psoriasis who participated in the phase 1, guselkumab first-in-human randomized, double-blind, placebo-controlled trial. At week 12, significant reductions in psoriasis gene expression were observed in guselkumab-treated patients.

2014-05-14 | GSE51440 | GEO

Gene expression patterns in blood during human anaphylaxis, trauma, and sepsis

Project description:Gene expression was profiled in peripheral blood samples collected from patients during anaphylaxis, trauma, or sepsis, and from healthy controls. Patients were recruited from three Australian emergency departments (ED) between March 2011 and June 2013. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2).

2021-09-12 | GSE69063 | 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