Summary of study ST000423

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 PR000331. The data can be accessed directly via it's Project DOI: 10.21228/M80S3Z This work is supported by NIH grant, U2C- DK119886.

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Study IDST000423
Study TitleDifferences in mycoplasma growth due to different mediums
Study SummaryThe object is to learn if there are variations in the lipid profiles of the three genomic variants (relative to one another) and if there are difference the lipid profiles due to growth in medium having different supplements. Mycoplasmas are eubacteria, but have only a single plasma membrane and no cell wall. They acquire FAs and cholesterol and other (perhaps many unknown) lipids from the medium which is complex and contains mammalian serum. Various mycoplasma species have been shown to contain a wide spectrum of bacterial lipids, but the composition is unknown for this mycoplasma species. We are particularly interested in ratios of membrane lipids among our strains, in part to gain clues about differences in metabolic pathways pertinent to membrane biogenesisÍž and to predict any underlying features that could relate to the extremely different modes of cell propagation observed among these genomic constructs.
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 Date2016-07-08
Num Groups4
Total Subjects24
Raw Data AvailableYes
Analysis Type DetailLC-MS
Release Date2016-09-23
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M80S3Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000331
Project DOI:doi: 10.21228/M80S3Z
Project Title:Differences in mycoplasma growth due to different mediums
Project Summary:The object is to learn if there are variations in the lipid profiles of the three genomic variants (relative to one another) and if there are difference the lipid profiles due to growth in medium having different supplements. Mycoplasmas are eubacteria, but have only a single plasma membrane and no cell wall. They acquire FAs and cholesterol and other (perhaps many unknown) lipids from the medium which is complex and contains mammalian serum. Various mycoplasma species have been shown to contain a wide spectrum of bacterial lipids, but the composition is unknown for this mycoplasma species. We are particularly interested in ratios of membrane lipids among our strains, in part to gain clues about differences in metabolic pathways pertinent to membrane biogenesisÍž and to predict any underlying features that could relate to the extremely different modes of cell propagation observed among these genomic constructs.
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:NIH U24DK097154

Subject:

Subject ID:SU000444
Subject Type:Bacteria
Subject Species:mycoplasma genomic variants
Taxonomy ID:10090
Species Group:Microorganism

Factors:

Subject type: Bacteria; Subject species: mycoplasma genomic variants (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA021537Quigley_Inj10_SA009Bone marrow macrophage
SA021538Quigley_Inj13_SA010Bone marrow macrophage
SA021539Quigley_Inj04_SA012Bone marrow macrophage
SA021540Quigley_Inj07_SA008Bone marrow macrophage
SA021541Quigley_Inj14_SA011Bone marrow macrophage
SA021542Quigley_Inj06_SA007Bone marrow macrophage
SA021543Quigley_Inj09_SA003Resident macrophage
SA021544Quigley_Inj03_SA002Resident macrophage
SA021545Quigley_Inj08_SA004Resident macrophage
SA021546Quigley_Inj11_SA005Resident macrophage
SA021547Quigley_Inj05_SA006Resident macrophage
SA021548Quigley_Inj12_SA001Resident macrophage
Showing results 1 to 12 of 12

Collection:

Collection ID:CO000438
Collection Summary:"Cells were centrifuged at 500g in PBS, the supernatant aspirated and the cell pellet snap frozen in liquid nitrogen"
Collection Protocol Filename:StudyDesign-LauraQuigley-121214.pdf
Sample Type:Cell

Treatment:

Treatment ID:TR000458
Treatment Summary:"Different cell types: 1. Peritoneal macrophages 2. Bone marrow derived macrophages"
Treatment Protocol Filename:StudyDesign-LauraQuigley-121214.pdf

Sample Preparation:

Sampleprep ID:SP000451
Sampleprep Summary:"1. Add 0.5mL of extraction solvent to tube, gently pipet to remove all cells, transfer cells to 2mL eppendorf tube. Repeat for a total of 1mL extraction solvent + cells in 2mL eppendorf tube. 2. Add 2 small stainless steel grinding beads to eppendorf tube 3. Use the GenoGrinder to grind for 3 minutes at 1,250 rpm. 4. Centrifuge at 14,000xg for 5 minutes. 5. Transfer supernatant to a fresh 2mL eppendorf tube. 6. Add 1mL of extraction solvent to tube containing cell pellet + beads, and repeat steps 3 and 4. 7. Collect supernatant, and combine with supernatant collected in step 5. Total volume of extracted sample will be approximately 2mL. 8. Dry down 50uL of extracted sample in 1.5mL eppendorf tube for GC-TOF analysis. 9. Store backups in -20 or -80C."
Sampleprep Protocol Filename:SOP_Extraction_of_Yeast_Cells.pdf

Combined analysis:

Analysis ID AN000671 AN000672
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 6530 Agilent 6550
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:CH000484
Chromatography Summary:UPLC
Methods Filename:Data Dictionary Fiehn laboratory_CSH QTOF lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6530
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:same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase
  
Chromatography ID:CH000485
Chromatography Summary:UPLC
Methods Filename:Data Dictionary Fiehn laboratory_CSH QTOF lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6550
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:5.0 uL
Solvent A:60:40 Acetonitrile:Water +10mM Ammonium Acetate +10mM Acetic Acid
Solvent B:9:1 Isopropanol:Acetonitrile +10mM Ammonium Acetate +10mM Acetic 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:same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000597
Analysis ID:AN000671
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs Lipidomics runs are performed in negative and positve mode (two filenames)
Ion Mode:POSITIVE
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
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350
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:MS000598
Analysis ID:AN000672
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs Lipidomics runs are performed in negative and positve mode (two filenames)
Ion Mode:NEGATIVE
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
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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