Summary of study ST000331

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 PR000265. The data can be accessed directly via it's Project DOI: 10.21228/M8J30W This work is supported by NIH grant, U2C- DK119886.

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Study IDST000331
Study TitleEffects of Zinc on GI tract metabolites (Part 2: Prostate)
Study SummaryThis experiment tested the affects of different diets on mice prostate metabolites. The diets ranged from zinc sufficient to zinc deficient and a third group that included zinc deficient mice that were put back on zinc sufficient diets.
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 Date2015-02-19
Num Groups6
Total Subjects48
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/M8J30W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000265
Project DOI:doi: 10.21228/M8J30W
Project Title:Effects of Zinc on GI tract metabolites
Project Summary:This experiment tested the affects of different diets on mice esophagus metabolites. The diets ranged from zinc sufficient to zinc deficient and a third group that included zinc deficient mice that were put back on zinc sufficient diets.
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:SU000351
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA014837P55Zn-Deficient
SA014838P56Zn-Deficient
SA014839P49Zn-Deficient
SA014840P54Zn-Deficient
SA014841P53Zn-Deficient
SA014842P51Zn-Deficient
SA014843P50Zn-Deficient
SA014844P52Zn-Deficient
SA014845P62Zn-replenished
SA014846P64Zn-replenished
SA014847P63Zn-replenished
SA014848P61Zn-replenished
SA014849P60Zn-replenished
SA014850P58Zn-replenished
SA014851P57Zn-replenished
SA014852P59Zn-replenished
SA014853P71Zn-sufficient
SA014854P72Zn-sufficient
SA014855P70Zn-sufficient
SA014856P67Zn-sufficient
SA014857P65Zn-sufficient
SA014858P66Zn-sufficient
SA014859P68Zn-sufficient
SA014860P69Zn-sufficient
Showing results 1 to 24 of 24

Collection:

Collection ID:CO000345
Collection Summary:At sacrifice, the genital urinary tract of male rats, comprising the bladder, urethra, seminal vesicles, and the prostate is excised, and microdissected under a dissecting microscope. The lateral prostate was removed, snapfrozen in liquid nitrogen, and stored at –80 °C.
Collection Protocol Filename:StudyDesign-LouiseFong-102314.pdf
Sample Type:Tissue

Treatment:

Treatment ID:TR000365
Treatment Summary:Three dietary Zn modulated groups: Zn deficient, Zn replenished,and control Zn sufficient Male weanling rats were fed a Zn deficient diet ad libitum (n = 16) or pairfed a control Zn sufficient diet (n = 8). After 6 weeks Zn deficient rats evidenced increased cell proliferation in the esophagus. Eight Zn deficient rats were switched immediately to the Zn sufficient diet to form the Zn replenished group. At 72 hours after replenishment, all animals (Zn deficient, Zn replenished, and Zn sufficient;n = 8/group) were killed. Note: Zn sufficient is the control group for each tissue (plasma, esophagus, or prostate)
Treatment Protocol Filename:StudyDesign-LouiseFong-102314.pdf

Sample Preparation:

Sampleprep ID:SP000359
Sampleprep Summary:1. Weigh 50 mg tissue sample in to a 25 ml conical polypropylene centrifuge tube. 2. Add 2.5mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent. 3. Centrifuge the samples at 2500 rpm. for 5 minutes. Aliquot 2 X 500µl supernatant, one for analysis and one for a backup sample. Store backup aliquot in the -20°C freezer. 4. Evaporate one 500µl aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness 5. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 6. Centrifuge for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 7. Remove supernatant to a new Eppendorff tube. 8. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 9. Submit to derivatization.
Sampleprep Protocol Filename:SOP_Extraction_of_Mammalian_Tissue_Samples.pdf

Combined analysis:

Analysis ID AN000529 AN000530
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:CH000369
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:MS000465
Analysis ID:AN000529
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:MS000466
Analysis ID:AN000530
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
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
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