MassIVE MSV000092601

Partial Public

GNPS - Metabolomics of novel Actinobacteria from oligotrophic subsurface soils

Description

There is a growing interest in the role of metabolite exchange (cross-feeding) in microbial community stability, resilience and longitudinal dynamics. Though the number of genome sequences available to researchers continues to grow, we still have a poor understanding of how to relate genomic information to exometabolite production/consumption capacity and how that capacity changes across different conditions. Our experimental design will be to obtain polar metabolomes and transcriptomes simultaneously from three conditions for each strain: Condition 1) mid-logarithmic phase (control); Condition 2) trace metal limited stationary phase; and Condition 3) nitrogen limited stationary phase. These experimental conditions were chosen because the bioavailability of trace metals and nitrogen in subsurface environments can be variable and nutrient availability has been shown to influence exometabolite profiles of Actinobacteria (Senges, et al 2018 PNAS). The work (proposal:https://doi.org/10.46936/10.25585/60001177) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. [doi:10.25345/C5SQ8QT68] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Actinobacteria, nitrogen limitation, subsurface, soil, trace metal limitation, metabolite exchange

Contact

Principal Investigators:
(in alphabetical order)
Paul Carini, University of Arizona, United States
Submitting User: bpbowen
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Experimental Design
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Identification Results
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Quantification Results
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GNPS content goes here (MSV000092601 [task=f763f9c31c9b4858895c0c0c09551990])
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.