Summary of Study ST000253
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 PR000205. The data can be accessed directly via it's Project DOI: 10.21228/M8WK5Q This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000253 |
| Study Title | NIH WCMC Pilot & Feasibility Project: Metabolomics of Neonatal Pulmonary Hypertension |
| Study Type | Treatment and feeding study |
| Study Summary | Targeted metabolomic analyses of oxylipins were performed on 16 rat plasma and lung samples collected from rats euthanized at 14 days following exposure to growth restriction and/or hyperoxia. Samples were analyzed by UPLC-MS/MS using a Waters Acquity UPLC and detected on an API 4000 QTrap (AB Sciex, Framingham, MA, USA) by multiple reaction monitoring (MRM) after negative mode electrospray ionization. |
| Institute | University of California, Davis |
| Department | U.S.D.A. Western Human Nutrition Research Center |
| Laboratory | Newman Lab |
| Last Name | Newman |
| First Name | John |
| Address | 430 W. Health Sciences Dr., Davis, CA 95616 |
| john.newman@ars.usda.gov | |
| Phone | +1-530-752-1009 |
| Submit Date | 2015-09-03 |
| Num Groups | 4 |
| Total Subjects | 16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Uploaded File Size | 16 M |
| Analysis Type Detail | LC-MS |
| Release Date | 2015-09-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000205 |
| Project DOI: | doi: 10.21228/M8WK5Q |
| Project Title: | Metabolomics of Neonatal Pulmonary Hypertension (in a Rat Model) |
| Project Type: | Treatment and feeding study |
| Project Summary: | This study aims to identify identify disrupted metabolic pathways and patterns of lung developent in a rat model of bronchopulmonary dysplasia and growth restriction. Pregnant Sprague Dawley rats (gestational day 15) were housed in plsatic cages under constant conditions. After 7-d acclimization period, litters were delivered and pups randomly distributed between litters of 10 pups (N, normal intake) or litters of 17 pups (R, restricted intake). Normal and restriced intake pups were exposed to 75% oxygen (O, oxygen) in a Plexiglass chamber or to 21% oxygen (A, room air) continuously for 14 days, with daily rotation of dams to avoid oxygen toxicity. Both plasma and lung tissue underwent metabolomics analysis. |
| Institute: | University of California, Davis |
| Department: | Department of Pediatrics, School of Medicine |
| Laboratory: | Wedgwood lab |
| Last Name: | Wedgwood |
| First Name: | Stephen |
| Address: | 1002B, Research II, 4625 2nd Ave., Sacramento, CA 95817 |
| Email: | stephen.wedwood@ucdmc.ucdavis.edu |
| Phone: | +1-916-734-1518 |
| Funding Source: | National Institute of Health U24 DK092993 |
Subject:
| Subject ID: | SU000273 |
| Subject Type: | Animal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Age Or Age Range: | 2 weeks |
| Animal Housing: | Litters of 10 (N group) or 17 (R group) |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Tissue |
|---|---|---|---|
| SA011542 | WEDG-1 | AN: Room Air, normal litter (no restricted nutritional intake) | Lung |
| SA011543 | WEDG-10 | AN: Room Air, normal litter (no restricted nutritional intake) | Lung |
| SA011544 | WEDG-7 | AN: Room Air, normal litter (no restricted nutritional intake) | Lung |
| SA011545 | WEDG-20 | AN: Room Air, normal litter (no restricted nutritional intake) | Lung |
| SA011546 | PAW-13 | AN: Room Air, normal litter (no restricted nutritional intake) | Plasma |
| SA011547 | PAW-8 | AN: Room Air, normal litter (no restricted nutritional intake) | Plasma |
| SA011548 | PAW-4 | AN: Room Air, normal litter (no restricted nutritional intake) | Plasma |
| SA011549 | PAW-16 | AN: Room Air, normal litter (no restricted nutritional intake) | Plasma |
| SA011550 | WEDG-17 | AR: Room Air, restricted intake | Lung |
| SA011551 | WEDG-19 | AR: Room Air, restricted intake | Lung |
| SA011552 | WEDG-6 | AR: Room Air, restricted intake | Lung |
| SA011553 | WEDG-15 | AR: Room Air, restricted intake | Lung |
| SA011554 | PAW-15 | AR: Room Air, restricted intake | Plasma |
| SA011555 | PAW-3 | AR: Room Air, restricted intake | Plasma |
| SA011556 | PAW-7 | AR: Room Air, restricted intake | Plasma |
| SA011557 | PAW-5 | AR: Room Air, restricted intake | Plasma |
| SA011558 | WEDG-3 | ON: 75% oxygen, normal litter | Lung |
| SA011559 | WEDG-14 | ON: 75% oxygen, normal litter | Lung |
| SA011560 | WEDG-18 | ON: 75% oxygen, normal litter | Lung |
| SA011561 | WEDG-2 | ON: 75% oxygen, normal litter | Lung |
| SA011562 | PAW-10 | ON: 75% oxygen, normal litter | Plasma |
| SA011563 | PAW-12 | ON: 75% oxygen, normal litter | Plasma |
| SA011564 | PAW-6 | ON: 75% oxygen, normal litter | Plasma |
| SA011565 | PAW-9 | ON: 75% oxygen, normal litter | Plasma |
| SA011566 | WEDG-11 | OR: 75% oxygen, restricted intake | Lung |
| SA011567 | WEDG-13 | OR: 75% oxygen, restricted intake | Lung |
| SA011568 | WEDG-9 | OR: 75% oxygen, restricted intake | Lung |
| SA011569 | WEDG-5 | OR: 75% oxygen, restricted intake | Lung |
| SA011570 | PAW-11 | OR: 75% oxygen, restricted intake | Plasma |
| SA011571 | PAW-14 | OR: 75% oxygen, restricted intake | Plasma |
| SA011572 | PAW-2 | OR: 75% oxygen, restricted intake | Plasma |
| SA011573 | PAW-1 | OR: 75% oxygen, restricted intake | Plasma |
| Showing results 1 to 32 of 32 |
Collection:
| Collection ID: | CO000265 |
| Collection Summary: | - |
| Collection Protocol Filename: | NewmanLab-F&BOxys-Protocol-PT.pdf |
| Sample Type: | Lung and plasma |
| Collection Method: | Dissection |
| Storage Conditions: | - 80°C |
| Storage Vials: | Eppendorf tubes |
Treatment:
| Treatment ID: | TR000285 |
| Treatment Summary: | Litters of 10 pups (N, normal intake) or litters of 17 pups (R, restricted intake). Normal and restriced intake pups were exposed to 75% oxygen (O, oxygen) in a Plexiglass chamber or to 21% oxygen (A, room air) continuously for 14 days, |
| Treatment Protocol Filename: | NewmanLab-F&BOxys-Protocol-PT.pdf |
| Treatment: | Intervention |
| Treatment Doseduration: | 1 week |
| Treatment Vehicle: | Food availability, oxygen exposure |
| Animal Endp Euthanasia: | 2 weeks |
| Animal Endp Tissue Coll List: | Lung and plasma |
| Animal Endp Tissue Proc Method: | Dissected, placed on dry ice |
Sample Preparation:
| Sampleprep ID: | SP000279 |
| Sampleprep Summary: | Tissues were pulverized on dry ice, enriched with deuterated surrogates, antioxidants (BHT and EDTA), and the total lipid extract was isolated using 10:8:11 cyclohexane/2-propanol/ammonium acetate (v/v/v). Subsequently, esterified oxylipins were liberated via sodium methoxide. Next, the remaining extract was eluted through a Waters Oasis-HLB cartridge. Plasma was added directly to a Waters Ostro plate, mixed with the surrogates, antioxidants, and acetonitrile and the extract eluted through. Both tissue and plasma extracts were dried, reconstituted in 100?L 50:50 methanol:acetonitrile with internal standards 1?phenyl?3?hexanoic acid urea and 1?cyclohexyl?3-dodecanoic acid urea (Sigma-Aldrich, St. Louis, MO) and filtered at 0.1 µm. |
| Sampleprep Protocol Filename: | NewmanLab-F&BOxys-Protocol-PT.pdf |
| Extraction Method: | Liquid:liquid with HLB solid phase extraction (Tissue); Ostro plate (Plasma) |
| Extract Cleanup: | HLB solid phase extraction (Tissue); Ostro plate (Plasma) |
| Extract Storage: | - 20 °C |
| Sample Resuspension: | 100 µL |
| Sample Spiking: | See sample prep protocol file |
| Organ: | Lung and plasma |
Combined analysis:
| Analysis ID | AN000400 | AN000401 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | ||
| Chromatography system | Waters Acquity | Waters Acquity |
| Column | ||
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap |
| Ion Mode | NEGATIVE | NEGATIVE |
| Units | % Area Ratio | nM |
Chromatography:
| Chromatography ID: | CH000283 |
| Chromatography Summary: | Oxylipin analysis |
| Methods Filename: | NewmanLab-F&BOxys-Protocol-PT.pdf |
| Instrument Name: | Waters Acquity |
| Column Temperature: | 60 C |
| Flow Gradient: | See protocol/methods file |
| Flow Rate: | 0.25 |
| Internal Standard: | See protocol/methods file |
| Retention Time: | See protocol/methods file |
| Sample Injection: | 5 L |
| Solvent A: | 100% water; 0.1% acetic acid |
| Solvent B: | 90% acetonitrile/ 10% isopropanol |
| Analytical Time: | 16 min |
| Weak Wash Solvent Name: | 20% methanol, 10% isopropanol |
| Weak Wash Volume: | 600 L |
| Strong Wash Solvent Name: | 50:50 Acetonitrile:Methanol |
| Strong Wash Volume: | 600 L |
| Sample Loop Size: | 17 L |
MS:
| MS ID: | MS000344 |
| Analysis ID: | AN000400 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Plasma results |
| Ion Mode: | NEGATIVE |
| MS ID: | MS000345 |
| Analysis ID: | AN000401 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Lung results |
| Ion Mode: | NEGATIVE |
