Summary of Study ST002381

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001531. The data can be accessed directly via it's Project DOI: 10.21228/M8ST4T This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002381
Study TitleRuegeria pomeroyi transporter mutant substrate drawdown
Study SummaryThe goal of this project was to identify bacterial transporters responsible for uptake of environmentally relevant marine metabolites. We used the model marine heterotrophic bacterium Ruegeria pomeroyi DSS-3, for which an arrayed library of single gene knockout mutants has been generated by selecting isolated from a barcoded transposon mutant library (BasSeq). Knockout mutants of putative transporters were grown on minimal medium with a single substrate as sole carbon source. Mutant defect was assessed by comparing the substrate drawdown of isolated mutants to drawdown by a pooled mutant library (BarSeq), a proxy for wildtype fitness.
Institute
University of Georgia
LaboratoryMoran Lab, Edison Lab
Last NameUchimiya
First NameMario
Address315 Riverbend Rd, Athens, GA, 30602, USA
Emailmario.uchimiya@uga.edu
Phone‭(706) 542-8387‬
Submit Date2022-11-16
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2022-12-27
Release Version1
Mario Uchimiya Mario Uchimiya
https://dx.doi.org/10.21228/M8ST4T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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NMR:

NMR ID:NM000256
Analysis ID:AN003880
Instrument Name:Bruker
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
NMR Comments:Analysis protocol: Instrument – Metabolites were analyzed by nuclear magnetic resonance (NMR) spectroscopy using a Bruker Avance lll 600 MHz spectrometer equipped with a 5-mm TCI cryoprobe. Data acquisition– Data were acquired by a one dimensional 1H experiment with water suppression (noesypr1d, Bruker) at 298K using TopSpin 3.6.4 (Bruker). For only glycerol, 1H J-resolved experiment (jresgpprqf) was used to avoid overlapping background peaks. Acquisition parameters are in ‘6_Acquisition and processing parameters_UGA_mutant_Nov2022.xlsx. Specific pulse programs used for individual samples are in ‘1_Study design_UGA_mutant_Nov2022.xlsx. Data processing – The raw Bruker spectra were processed using NMRPipe on NMRbox. For Jres, spectra were further symmetrized and tilted. Detailed spectrum processing parameters for individual NMR experiments are in ‘6_Acquisition and processing parameters_UGA_mutant_Nov2022.xlsx. NMRPipe scripts are available in folder ‘Data_analysis’. Downstream data analysis: Downstream analysis was conducted using Metabolomics Toolbox (https://github.com/artedison/Edison_Lab_Shared_Metabolomics_UGA) and MATLAB R2022a (MathWorks). All the input files, processing steps and scripts, and the output files are available in folder ‘Data_analysis’.
Spectrometer Frequency:600 MHz
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