Summary of study ST000330

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 IDST000330
Study TitleEffects of Zinc on GI tract metabolites (Part 1: Esophagus)
Study SummaryThis 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
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 Date2015-02-18
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:SU000350
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
SA014813P31Zn-Deficient
SA014814P32Zn-Deficient
SA014815P25Zn-Deficient
SA014816P30Zn-Deficient
SA014817P29Zn-Deficient
SA014818P27Zn-Deficient
SA014819P26Zn-Deficient
SA014820P28Zn-Deficient
SA014821P38Zn-replenished
SA014822P40Zn-replenished
SA014823P39Zn-replenished
SA014824P37Zn-replenished
SA014825P36Zn-replenished
SA014826P34Zn-replenished
SA014827P33Zn-replenished
SA014828P35Zn-replenished
SA014829P47Zn-sufficient
SA014830P48Zn-sufficient
SA014831P46Zn-sufficient
SA014832P43Zn-sufficient
SA014833P41Zn-sufficient
SA014834P42Zn-sufficient
SA014835P44Zn-sufficient
SA014836P45Zn-sufficient
Showing results 1 to 24 of 24

Collection:

Collection ID:CO000344
Collection Summary:At sacrifice, esophagi were isolated. Esophageal epithelium was prepared by using a blade to remove the submucosal and muscularis layers, snapfrozen in liquid nitrogen, and stored at –80 °C.
Collection Protocol Filename:StudyDesign-LouiseFong-102314.pdf
Sample Type:Tissue

Treatment:

Treatment ID:TR000364
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:SP000358
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 AN000527 AN000528
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:CH000368
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:MS000463
Analysis ID:AN000527
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:MS000464
Analysis ID:AN000528
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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