Summary of Study ST000324
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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000324 |
| Study Title | Progesterone level effects on primary metabolites in uterus, blood, and ovaries (Part 3:Ovaries) |
| Study 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 ovaries (follicle fluid) 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 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2015-03-16 |
| Num Groups | 1 |
| Total Subjects | 20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-01-27 |
| Release Version | 1 |
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: | SU000344 |
| 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 |
|---|---|---|
| SA014652 | 198 | Follicle Fluid |
| SA014653 | 199 | Follicle Fluid |
| SA014654 | 200 | Follicle Fluid |
| SA014655 | 197 | Follicle Fluid |
| SA014656 | 196 | Follicle Fluid |
| SA014657 | 192 | Follicle Fluid |
| SA014658 | 193 | Follicle Fluid |
| SA014659 | 194 | Follicle Fluid |
| SA014660 | 195 | Follicle Fluid |
| SA014661 | 191 | Follicle Fluid |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO000338 |
| Collection Summary: | Follicular Fluid: Follicular Fluid were obtained by postmortem aspiration of the ovarian dominant follicle and kept at 80ºC. There was no inactivation or attenuation because samples are not biohazard. |
| Collection Protocol Filename: | StudyDesign-MarioBinelli-101414.pdf |
| Sample Type: | Follicular fluid |
Treatment:
| Treatment ID: | TR000358 |
| 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: | SP000352 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Mammalian_Tissue_Samples.pdf |
Combined analysis:
| Analysis ID | AN000516 | AN000517 |
|---|---|---|
| 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: | CH000362 |
| 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: | MS000452 |
| Analysis ID: | AN000516 |
| 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: | MS000453 |
| Analysis ID: | AN000517 |
| 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 |
