Summary of study ST000322

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 PR000261. The data can be accessed directly via it's Project DOI: 10.21228/M8230J This work is supported by NIH grant, U2C- DK119886.

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Study IDST000322
Study TitleProgesterone level effects on primary metabolites in uterus, blood, and ovaries (Part 1:Plasma)
Study SummaryIn this experiment a hormonal protocol was applied to control follicle growth to yield larger or smaller preovulatory follicle and CLs and consequently different circulating Progesterone (P4) concentrations during early diestrus. The two different animal's group are: high or low progesterone levels. The effects of these progesterone levels was tested in the blood of the cow.
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 Date2015-03-16
Num Groups1
Total Subjects80
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/M8230J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000261
Project DOI:doi: 10.21228/M8230J
Project Title:Progesterone level effects on primary metabolites in uterus, blood, and ovaries
Project Summary:In this experiment a hormonal protocol was applied to control follicle growth to yield larger or smaller preovulatory follicle and CLs and consequently different circulating Progesterone (P4) concentrations during early diestrus. The two different animal's group are: high or low progesterone levels. The effects of these progesterone levels was tested in the uterus, blood, and ovaries of the cow.
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:SU000342
Subject Type:Animal
Subject Species:Bos taurus
Taxonomy ID:9913
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Bos taurus (Factor headings shown in green)

mb_sample_id local_sample_id Organ
SA01454255Plasma
SA01454354Plasma
SA01454453Plasma
SA01454556Plasma
SA01454658Plasma
SA01454760Plasma
SA01454859Plasma
SA01454952Plasma
SA01455057Plasma
SA01455150Plasma
SA01455245Plasma
SA01455344Plasma
SA01455443Plasma
SA01455546Plasma
SA01455647Plasma
SA014557101Plasma
SA01455849Plasma
SA01455948Plasma
SA01456051Plasma
SA014561103Plasma
SA014562155Plasma
SA014563154Plasma
SA014564153Plasma
SA014565156Plasma
SA014566157Plasma
SA014567160Plasma
SA014568159Plasma
SA014569158Plasma
SA014570152Plasma
SA014571151Plasma
SA014572105Plasma
SA014573104Plasma
SA01457442Plasma
SA014575106Plasma
SA014576107Plasma
SA014577110Plasma
SA014578109Plasma
SA014579108Plasma
SA014580102Plasma
SA01458141Plasma
SA01458215Plasma
SA01458314Plasma
SA01458413Plasma
SA01458512Plasma
SA01458616Plasma
SA01458717Plasma
SA01458820Plasma
SA01458919Plasma
SA01459018Plasma
SA01459111Plasma
SA01459210Plasma
SA0145934Plasma
SA0145943Plasma
SA0145952Plasma
SA0145965Plasma
SA0145976Plasma
SA0145989Plasma
SA0145998Plasma
SA0146007Plasma
SA01460121Plasma
SA01460222Plasma
SA01460335Plasma
SA01460434Plasma
SA01460533Plasma
SA01460636Plasma
SA01460737Plasma
SA01460840Plasma
SA01460939Plasma
SA01461038Plasma
SA01461132Plasma
SA01461231Plasma
SA01461325Plasma
SA01461424Plasma
SA01461523Plasma
SA01461626Plasma
SA01461727Plasma
SA01461830Plasma
SA01461929Plasma
SA01462028Plasma
SA0146211Plasma
Showing results 1 to 80 of 80

Collection:

Collection ID:CO000336
Collection Summary:Plasma: plasma were obtained by centrifugation of the blood collected from cows and kept at 80ÂșC. There was no inactivation or attenuation because samples are not biohazard.
Collection Protocol Filename:StudyDesign-MarioBinelli-101414.pdf
Sample Type:Plasma

Treatment:

Treatment ID:TR000356
Treatment Summary:There was no specific treatment. A hormonal protocol was applied to control follicle growth to yield larger or smaller preovulatory follicle and CLs and consequently different circulating Progesterone (P4) concentrations during early diestrus. The two different animal's group are: high or low progesterone levels.
Treatment Protocol Filename:StudyDesign-MarioBinelli-101414.pdf

Sample Preparation:

Sampleprep ID:SP000350
Sampleprep Summary:-
Sampleprep Protocol Filename:SOP_Extraction_of_Blood_Samples.pdf

Combined analysis:

Analysis ID AN000512 AN000513
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:CH000360
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:MS000448
Analysis ID:AN000512
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
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:MS000449
Analysis ID:AN000513
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
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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