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.
Study ID | ST002381 |
Study Title | Ruegeria pomeroyi transporter mutant substrate drawdown |
Study Summary | The 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 |
Laboratory | Moran Lab, Edison Lab |
Last Name | Uchimiya |
First Name | Mario |
Address | 315 Riverbend Rd, Athens, GA, 30602, USA |
mario.uchimiya@uga.edu | |
Phone | (706) 542-8387 |
Submit Date | 2022-11-16 |
Raw Data Available | Yes |
Raw Data File Type(s) | fid |
Analysis Type Detail | NMR |
Release Date | 2022-12-27 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |