Summary of study ST000318

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 PR000257. The data can be accessed directly via it's Project DOI: 10.21228/M8K306 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000318
Study TitleAllantoin differences in Synechococcus cells grown in high versus low lightgrowth
Study SummaryThis experimented consisted of analysis of 500-1000ml of Synechococcus dense cell cultures grown in high versus low light. The goal was to see any differences in the metabolites between the two treatments, especially with respect to Allantoin.
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 Date2014-11-14
Num Groups4
Total Subjects12
Raw Data AvailableYes
Raw Data File Type(s).bin,.xsd,.cd,.cg,.xml
Analysis Type DetailLC-MS
Release Date2016-01-27
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8K306
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000257
Project DOI:doi: 10.21228/M8K306
Project Title:Allantoin differences in Synechococcus cells grown in high versus low light
Project Summary:This experimented consisted of analysis of 500-1000ml of Synechococcus dense cell cultures grown in high versus low light. The goal was to see any differences in the metabolites between the two treatments, especially with respect to Allantoin.
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:SU000338
Subject Type:Bacterial cells
Subject Species:Synechococcus sp CC9605
Species Group:Microorganism

Factors:

Subject type: Bacterial cells; Subject species: Synechococcus sp CC9605 (Factor headings shown in green)

mb_sample_id local_sample_id Light treatment
SA0144906DD
SA0144915DD
SA0144924DD
SA0144932LL
SA0144943LL
SA0144951LL
Showing results 1 to 6 of 6

Collection:

Collection ID:CO000332
Collection Summary:-
Sample Type:Cells

Treatment:

Treatment ID:TR000352
Treatment Summary:Cells grown in high versus low light
Treatment Protocol Filename:StudyDesign_BrianPalenik_081914.pdf

Sample Preparation:

Sampleprep ID:SP000346
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_Cell_pellets.pdf

Combined analysis:

Analysis ID AN000505 AN000506
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Unspecified Unspecified
Column Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak height Peak height

Chromatography:

Chromatography ID:CH000356
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Unspecified
Column Name:Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:1.67 uL
Solvent A:60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid
Solvent B:9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid
Analytical Time:13 min
Capillary Voltage:3500
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Isopropanol
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000441
Analysis ID:AN000505
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 l/min
Dry Gas Temp:325
Fragment Voltage:120
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Pos
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000442
Analysis ID:AN000506
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:13 l/min
Dry Gas Temp:200
Fragment Voltage:175
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Neg
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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