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.

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Study IDST001305
Study TitleIntegrated Metabolomics and Transcriptomics Suggest the Global Metabolic Response to 2-Aminoacrylate Stress in Salmonella enterica
Study SummaryNMR metabolomics of bacterial extractions from WT and 2-iminobutanoate/2iminopropanoate deaminase (RidA) KO S. Enterica lines
Institute
University of Georgia
DepartmentCCRC
Last NameEdison
First NameArthur
Address315 Riverbend Road, Athens, GA 30602
Emailaedison@uga.edu
Phone7065428156
Submit Date2020-01-09
Num Groups2
Total Subjects19
Raw Data AvailableYes
Raw Data File Type(s)._procs, ._acqu, pdata
Analysis Type DetailNMR
Release Date2020-03-03
Release Version1
Arthur Edison Arthur Edison
https://dx.doi.org/10.21228/M85D77
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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

Factors:

Subject type: Bacteria; Subject species: Salmonella enterica (Factor headings shown in green)

mb_sample_id local_sample_id Strain
SA094367RidA8RidA KO
SA094368RidA9RidA KO
SA094369RidA1RidA KO
SA094370RidA6RidA KO
SA094371RidA7RidA KO
SA094372RidA2RidA KO
SA094373RidA4RidA KO
SA094374RidA3RidA KO
SA094375RidA5RidA KO
SA094376WT7WT
SA094377WT8WT
SA094378WT9WT
SA094379WT6WT
SA094380WT1WT
SA094381WT2WT
SA094382WT3WT
SA094383WT4WT
SA094384WT5WT
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
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