Summary of Study ST000328

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 PR000263. The data can be accessed directly via it's Project DOI: 10.21228/M8SK5S This work is supported by NIH grant, U2C- DK119886.

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Study IDST000328
Study TitlePrimary metabolites at different points along dog gastrointestinal tract (CSH chromatography)
Study SummaryThis experiment tests the primary metabolites at four different points along the gastrointestinal tract of a dog. The four points being tested were the duodenum, ileum, colon, and rectum.
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 Date2015-02-12
Num Groups8
Total Subjects48
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-01-27
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8SK5S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000263
Project DOI:doi: 10.21228/M8SK5S
Project Title:Primary metabolites at different points along dog gastrointestinal tract
Project Summary:This experiment tests the primary metabolites at four different points along the gastrointestinal tract of a dog. The four points being tested were the duodenum, ileum, colon, and rectum.
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:SU000348
Subject Type:Animal
Subject Species:Canis lupus familiaris
Taxonomy ID:9615
Species Group:Mammals

Factors:

Subject type: Animal; Subject species: Canis lupus familiaris (Factor headings shown in green)

mb_sample_id local_sample_id Organ
SA014759D_colonColon
SA014760E_colonColon
SA014761G_colonColon
SA014762C_colonColon
SA014763F_colonColon
SA014764A_colonColon
SA014765G_duodDuodenum
SA014766E_duodDuodenum
SA014767D_duodDuodenum
SA014768C_duodDuodenum
SA014769A_duodDuodenum
SA014770F_duodDuodenum
SA014771A_ileumIleum
SA014772D_ileumIleum
SA014773E_ileumIleum
SA014774F_ileumIleum
SA014775G_ileumIleum
SA014776C_ileumIleum
SA014777G_rectumRectum
SA014778F_rectumRectum
SA014779A_rectumRectum
SA014780C_rectumRectum
SA014781D_rectumRectum
SA014782E_rectumRectum
Showing results 1 to 24 of 24

Collection:

Collection ID:CO000342
Collection Summary:Samples were collected from dogs euthanized for an unrelated reason. From 6 different dogs, samples were taken from 4 different sites along the gastrointestinal tract (calling these treatments). Samples were frozen at ­80, then thawed to aliquot into 100mg portions, and refrozen at ­80 and shipped on dry ice. No other preparation/additives. Samples were collected from dogs euthanized for an unrelated reason. From 6 different dogs, samples were taken from 4 different sites along the gastrointestinal tract (calling these treatments). Samples were frozen at ­80, then thawed to aliquot into 100mg portions, and refrozen at ­80 and shipped on dry ice. No other preparation/additives.
Collection Protocol Filename:StudyDesign-JuliaHonneffer-101614.pdf
Sample Type:Tissue (duodenum, illium, colon, rectum)

Treatment:

Treatment ID:TR000362
Treatment Summary:4 x 6; Different sites along the gastrointestinal tract (duodenum, ileum, colon, rectum)
Treatment Protocol Filename:StudyDesign-JuliaHonneffer-101614.pdf

Sample Preparation:

Sampleprep ID:SP000356
Sampleprep Summary:-

Combined analysis:

Analysis ID AN000523 AN000524
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:CH000366
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% 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:Isopropanol
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000459
Analysis ID:AN000523
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:MS000460
Analysis ID:AN000524
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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