Summary of Study ST000326

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 PR000256. The data can be accessed directly via it's Project DOI: 10.21228/M8PS35 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000326
Study TitleRole of medium in bacterial growth (HILIC chromatography)
Study SummaryExperiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2014-11-25
Num Groups4
Total Subjects38
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-01-27
Release Version2
Release CommentsUpdated study design factors
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8PS35
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000256
Project DOI:doi: 10.21228/M8PS35
Project Title:Role of medium in bacterial growth
Project Summary:Experiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:U24DK097154

Subject:

Subject ID:SU000346
Subject Type:Bacterial cells
Subject Species:Bacteria
Species Group:Bacteria

Factors:

Subject type: Bacterial cells; Subject species: Bacteria (Factor headings shown in green)

mb_sample_id local_sample_id labeltype
SA014716SA012A
SA014717SA013A
SA014718SA014A
SA014719SA015A
SA014720SA016A
SA014721SA017A
SA014722SA018A
SA014723SA019A
SA014724SA001E
SA014725SA010E
SA014726SA011E
SA014727SA002E
SA014728SA003E
SA014729SA004E
SA014730SA005E
SA014731SA006E
SA014732SA007E
SA014733SA008E
SA014734SA009E
Showing results 1 to 19 of 19

Collection:

Collection ID:CO000340
Collection Summary:-
Sample Type:spent culture supernatant

Treatment:

Treatment ID:TR000360
Treatment Summary:There are 2 treatments. Each sample is a supernatant from a different bacterial strain grown in culture.There are a total of 17 strains, 10 of which are grown in one type of medium and 7 are grown in another type of medium. Supernatants from the 2 types of media are also submitted for analysis.
Treatment Protocol Filename:StudyDesign_NadirMahmood_072914.pdf

Sample Preparation:

Sampleprep ID:SP000354
Sampleprep Summary:1. After quenching the cells add 1 X 106 dried cells to 1.5 ml eppendorff tube. 2. Place the eppendorf tube with cells on dry ice for 20 minutes or til the cells are completely frozen and ice for 20 minutes, till they are completely thawed. Repeat this step twice. 3. Add 1ml of extraction solvent which has been pre-chilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. to the ependorff tube with cells. 4. Repeat step 2 twice with the extraction solvent. 5. Vortex the sample for 10s and shake for 5min at 4°C using the Orbital Mixing Chilling/Heating plate. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 500µL portions of the supernatant. One for analysis and one for backup. Store one aliquot in the -20°C freezer as a backup. 7. Evaporate one 500µL aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. Submit to derivatization
Sampleprep Protocol Filename:SOP_Extraction_of_Mammalian_Tissue_Samples.pdf

Chromatography:

Chromatography ID:CH000364
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_HILIC_QTOF_MS.pdf
Instrument Name:Unspecified
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Pressure:200-700 bar
Column Temperature:45 C
Flow Gradient:100% B to 30% B
Flow Rate:0.4 mL/min
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:3 uL
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3
Solvent B:95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate, pH 3
Analytical Time:14 min
Capillary Voltage:4500
Time Program:16.75 min
Weak Wash Solvent Name:1:1 ACN:H2O
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:1:1 ACN:H2O
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:HILIC

Analysis:

Analysis ID:AN000519
Laboratory Name:WCMC Metabolomics Core
Analysis Type:MS
Instrument Name:Agilent 6530 QTOF
Software Version:MassHunter
Detector Type:TOF MCP
Data Format:.d
Chromatography ID:CH000364
Num Factors:2
Num Metabolites:22
Rt Units:Minutes
Units:Peak height
  
Analysis ID:AN000520
Laboratory Name:WCMC Metabolomics Core
Analysis Type:MS
Instrument Name:Agilent 6550 QTOF
Software Version:MassHunter
Detector Type:TOF MCP
Data Format:.d
Chromatography ID:CH000364
Num Factors:2
Rt Units:Minutes
Units:Peak height
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