Summary of Study ST000354

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 PR000283. The data can be accessed directly via it's Project DOI: 10.21228/M8BC8T This work is supported by NIH grant, U2C- DK119886.

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Study IDST000354
Study TitleMetabolite comparison of mouse gastric tissue and glands
Study SummaryThe goal of this project was to compare the metabolite profiles of the: mouse gastric antrum and the mouse gastric corpus, the mouse gastric antrum and the mouse gastric antrum isolated glands, and the mouse gastric corpus and the mouse gastric corpus isolated glands.
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 Date2016-02-09
Num Groups8
Total Subjects32
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-03-03
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8BC8T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000283
Project DOI:doi: 10.21228/M8BC8T
Project Title:Metabolite comparison of mouse gastric tissue and glands
Project Summary:The goal of this project was to compare the metabolite profiles of the: mouse gastric antrum and the mouse gastric corpus, the mouse gastric antrum and the mouse gastric antrum isolated glands, and the mouse gastric corpus and the mouse gastric corpus isolated glands.
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:SU000374
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Organ
SA0154938Antrum
SA01549410Antrum
SA01549512Antrum
SA0154967Antrum
SA01549711Antrum
SA0154989Antrum
SA01549915Antrum Glands
SA01550016Antrum Glands
SA0155016Corpus
SA0155025Corpus
SA0155031Corpus
SA0155042Corpus
SA0155054Corpus
SA0155063Corpus
SA01550714Corpus Glands
SA01550813Corpus Glands
SA015509Pool04Plasma
SA015510Biorec02Plasma
SA015511Pool03Plasma
SA015512Pool02Plasma
SA015513Biorec01Plasma
SA015514Pool01Plasma
SA015515Biorec03Plasma
Showing results 1 to 23 of 23

Collection:

Collection ID:CO000368
Collection Summary:The gastric samples (A and C) were prepared by dissecting tissue from the mouse, rinsing in PBS, and flash freezing on liquid N2. The samples were stored at ­80 C. The glands samples (Aglands and Cglands) by isolating gastric glands from mouse stomach tissue using EDTA and Sucrose and sorbitol. The glands were centrifuged and the supernatant removed, but there is probably still sucrose and sorbitol left. These were flash frozen on liquid N2 and stored at ­80 C.
Collection Protocol Filename:StudyDesign-KarenOttemann-81215-1.pdf
Sample Type:Tissue

Treatment:

Treatment ID:TR000388
Treatment Summary:A. Mouse gastric antrum (n=6) C. Mouse gastric corpus (n=6) Aglands. Mouse gastric antrum isolated glands (n=2) Cglands. Mouse gastric corpus isolated glands (n=2)
Treatment Protocol Filename:StudyDesign-KarenOttemann-81215-1.pdf

Sample Preparation:

Sampleprep ID:SP000381
Sampleprep Summary:None

Combined analysis:

Analysis ID AN000577 AN000578
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:CH000412
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% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate
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:CH000413
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:40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 10mM acetic acid; 10mM ammonium acetate
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:MS000513
Analysis ID:AN000577
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
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
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000514
Analysis ID:AN000578
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are performed in negative and positve mode (two filenames)
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
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
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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