Summary of Study ST001305
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 PR000886. The data can be accessed directly via it's Project DOI: 10.21228/M85D77 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001305 |
| Study Title | Integrated Metabolomics and Transcriptomics Suggest the Global Metabolic Response to 2-Aminoacrylate Stress in Salmonella enterica |
| Study Summary | NMR metabolomics of bacterial extractions from WT and 2-iminobutanoate/2iminopropanoate deaminase (RidA) KO S. Enterica lines |
| Institute | University of Georgia |
| Department | CCRC |
| Last Name | Edison |
| First Name | Arthur |
| Address | 315 Riverbend Road, Athens, GA 30602 |
| aedison@uga.edu | |
| Phone | 7065428156 |
| Submit Date | 2020-01-09 |
| Num Groups | 2 |
| Total Subjects | 19 |
| Raw Data Available | Yes |
| Analysis Type Detail | NMR |
| Release Date | 2020-03-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000886 |
| Project DOI: | doi: 10.21228/M85D77 |
| Project Title: | Intergrated Metabolomics and Transcriptomics Suggest Global Metabolic Response to 2-Aminoacrylate Stress in Salmonella enterica |
| Project Type: | Comparison |
| Project Summary: | Bacterial extractions from WT and 2-iminobutanoate/2iminopropanoate deaminase (RidA) KO S. Enterica lines |
| Institute: | University of Georgia |
| Department: | CCRC |
| Last Name: | Walejko |
| First Name: | Jacquelyn |
| Address: | 315 Riverbend Road, Rm 1045, Athens GA 30602 |
| Email: | jacquelyn.walejko@duke.edu |
| Phone: | 9194792304 |
Subject:
| Subject ID: | SU001379 |
| Subject Type: | Bacteria |
| Subject Species: | Salmonella enterica |
| Taxonomy ID: | 28901 |
| Species Group: | Bacteria |
Factors:
Subject type: Bacteria; Subject species: Salmonella enterica (Factor headings shown in green)
| mb_sample_id | local_sample_id | Strain |
|---|---|---|
| SA094367 | RidA8 | RidA KO |
| SA094368 | RidA9 | RidA KO |
| SA094369 | RidA1 | RidA KO |
| SA094370 | RidA6 | RidA KO |
| SA094371 | RidA7 | RidA KO |
| SA094372 | RidA2 | RidA KO |
| SA094373 | RidA4 | RidA KO |
| SA094374 | RidA3 | RidA KO |
| SA094375 | RidA5 | RidA KO |
| SA094376 | WT7 | WT |
| SA094377 | WT8 | WT |
| SA094378 | WT9 | WT |
| SA094379 | WT6 | WT |
| SA094380 | WT1 | WT |
| SA094381 | WT2 | WT |
| SA094382 | WT3 | WT |
| SA094383 | WT4 | WT |
| SA094384 | WT5 | WT |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO001374 |
| Collection Summary: | Ten biologically independent cultures each of wild-type (DM9404) and ridA mutant (DM3480) strains were grown overnight in NB medium at 37 °C and used to inoculate (1% inoculum) 250 mL minimal glucose medium in 500 mL non-baffled flasks. Flasks were randomly arranged in an Innova®44 incubator and cultures were allowed to grow 16 h shaking at 180 RPM and 37 °C. Cultures were cooled on ice 5 min and then harvested by centrifugation at 7,000 x G for 10 min at 4 °C. The supernatant was decanted, pellets were resuspended in 10 mL ddH2O and transferred to sterile 15 mL conical tubes in which they were pelleted at 7,000 x G 10 min at 4 °C. Final supernatant was decanted and pellets were frozen in liquid nitrogen and stored at -80 °C prior to cell extractions. |
| Sample Type: | Bacterial cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001394 |
| Treatment Summary: | These samples did not undergo addition treatment. |
Sample Preparation:
| Sampleprep ID: | SP001387 |
| Sampleprep Summary: | Each frozen bacterial pellet (~1 g) was thawed on ice and homogenized 3 times. For homogenization, 2.6 g of 0.1 mm zirconium beads and 6 mL 4 C MeOH/H2O (80/20) solvent was added and samples were agitated 7 times (210 s total) at 1600 rpm in a FastPrep 96 (MPBIO). Samples were then centrifuged at 416 g and 4 C for 16 min and supernatant was transferred to a new 15 mL conical tube. Homogenization was carried out a second and third time using 4 mL MeOH/H2O with 4 homogenization cycles (150 s) and 2 mL MeOH/H2O with 3 homogenization cycles (150 s), respectively. Pooled supernatants from each sample were concentrated to dryness using a CentriVap Benchtop Vacuum Concentrator (Labconco). The extracts were reconstituted in 600 L of deuterated 100 mM sodium phosphate bu er (pH 7.4) containing 1 mM of the internal standard DSS (d6 4,4-dimethyl-4-silapentane-1-sulfonic acid) and vortex mixed 2 min. Each sample was transferred into 5 mm SampleJet NMR tubes for NMR analysis. |
Analysis:
| Analysis ID: | AN002174 |
| Laboratory Name: | Complex Carbohydrate Research Center NMR Facility |
| Analysis Type: | NMR |
| Operator Name: | Adrien Le Guennec |
| Num Factors: | 2 |
| Num Metabolites: | 37 |
| Units: | Area Under Curve |
NMR:
| NMR ID: | NM000159 |
| Analysis ID: | AN002174 |
| Instrument Name: | Bruker Avance III HD |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 800 MHz |
