Summary of Study ST002043

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 PR001290. The data can be accessed directly via it's Project DOI: 10.21228/M8ZQ4B This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002043
Study TitleMaternal Hypoxemia and Oxidative Stress
Study Typeuntargeted metabolomics
Study SummaryThis project seeks to understand the metabolic consequences of gestational hypoxia on fetal, newborn, and adult plasma, arteries and other tissues using a sheep model of fetal growth restriction. Specifically we are interested testing the hypothesis that gestational hypoxia will result in discernable differences in glucose and lipid metabolism in tissues and plasma as well influence indicators of oxidative stress and inflammation. These studies aim to delineate pathways and biomarkers that help explain how hypoxia leads to the development of neonatal as well as adult-onset diseases associated with chronic hypoxia that are inter-related with fetal growth restriction. From a vascular perspective this includes cerebrovascular hemorrhage and pulmonary hypertension in the newborn, but more broadly it includes development of diseases later in life including diabetes, hypertension, and coronary artery disease.
Institute
Loma Linda University School of Medicine
DepartmentLawrence D. Longo, MD Center for Perinatal Biology
LaboratorySean Wilson, Center for Perinatal Biology
Last NameWilson
First NameSean
Address11234 Anderson Street, MC A582, Loma Linda, California 92350
Emailseanwilson@llu.edu
Phone909-558-4325
Submit Date2021-12-01
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2022-01-21
Release Version1
Sean Wilson Sean Wilson
https://dx.doi.org/10.21228/M8ZQ4B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001290
Project DOI:doi: 10.21228/M8ZQ4B
Project Title:Maternal Hypoxemia and Oxidative Stress
Project Summary:This project seeks to understand the metabolic consequences of gestational hypoxia on fetal, newborn, and adult plasma, arteries and other tissues using a sheep model of fetal growth restriction. Specifically we are interested testing the hypothesis that gestational hypoxia will result in discernable differences in glucose and lipid metabolism in tissues and plasma as well influence indicators of oxidative stress and inflammation. These studies aim to delineate pathways and biomarkers that help explain how hypoxia leads to the development of neonatal as well as adult-onset diseases associated with chronic hypoxia that are inter-related with fetal growth restriction. From a vascular perspective this includes cerebrovascular hemorrhage and pulmonary hypertension in the newborn, but more broadly it includes development of diseases later in life including diabetes, hypertension, and coronary artery disease.
Institute:LOMA LINDA UNIVERSITY
Department:Lawrence D. Longo, MD Center for Perinatal Biology
Laboratory:Sean Wilson, Center for Perinatal Biology
Last Name:Wilson
First Name:Sean
Address:11234 Anderson Street, MC A582, Loma Linda, California 92350
Email:seanwilson@llu.edu
Phone:909-558-4325
Funding Source:WCMC Pilot Project (U24DK097154), P01HD083132

Subject:

Subject ID:SU002125
Subject Type:Mammal
Subject Species:Ovis aries
Taxonomy ID:9940

Factors:

Subject type: Mammal; Subject species: Ovis aries (Factor headings shown in green)

mb_sample_id local_sample_id treatment
SA191949SW27_091Control Fetal
SA191950SW25_089Control Fetal
SA191951C101G_045Control Fetal
SA191952SW29_093Control Fetal
SA191953SW40_104Control Fetal
SA191954SW42_106Control Fetal
SA191955WJP18_038Control Fetal
SA191956SW41_105Control Fetal
SA191957WJP20_040Control Fetal
SA191958WJP19_039Control Fetal
SA191959C162G_041Control Fetal
SA191960C119G_043Control Fetal
SA191961C105G-F1_046Control Fetal
SA191962C174G_042Control Fetal
SA191963C194G_044Control Fetal
SA191964WJP16_036Control Fetal
SA191965WJP17_037Control Fetal
SA191966SW31_095Control New Born
SA191967L#89B_058Control New Born
SA191968C263R_055Control New Born
SA191969SW7_071Control New Born
SA191970C264R_054Control New Born
SA191971SW8_072Control New Born
SA191972L#86B_056Control New Born
SA191973L#87B_057Control New Born
SA191974LZ2_002Control Non-preg
SA191975LZ3_003Control Non-preg
SA191976LZ4_004Control Non-preg
SA191977SW15_079Control Non-preg
SA191978LZ5_005Control Non-preg
SA191979SW37_101Control Non-preg
SA191980SW38_102Control Non-preg
SA191981LZ1_001Control Non-preg
SA191982SW17_081Control Non-preg
SA191983SW16_080Control Non-preg
SA191984SW18_082Control Non-preg
SA191985WJP13_033Control Non-preg
SA191986WJP12_032Control Non-preg
SA191987WJP11_031Control Non-preg
SA191988WJP14_034Control Non-preg
SA191989WJP15_035Control Non-preg
SA191990LZ8_008Control Preg
SA191991LZ6_006Control Preg
SA191992LZ7_007Control Preg
SA191993LZ9_009Control Preg
SA191994LZ10_010Control Preg
SA191995SW24_088Hypoxic Fetal
SA191996SW20_084Hypoxic Fetal
SA191997WM103G_051Hypoxic Fetal
SA191998SW21_085Hypoxic Fetal
SA191999SW39_103Hypoxic Fetal
SA192000WM18G_052Hypoxic Fetal
SA192001WM142R-F2_049Hypoxic Fetal
SA192002WM142R-F1_047Hypoxic Fetal
SA192003WM145R_050Hypoxic Fetal
SA192004SW19_083Hypoxic Fetal
SA192005WM1G_048Hypoxic Fetal
SA192006WM91G-F1_053Hypoxic Fetal
SA192007SW23_087Hypoxic Fetal
SA192008WJP10_030Hypoxic Fetal
SA192009WJP8_028Hypoxic Fetal
SA192010WJP6_026Hypoxic Fetal
SA192011WJP7_027Hypoxic Fetal
SA192012WJP9_029Hypoxic Fetal
SA192013SW10_074Hypoxic New Born
SA192014SW32_096Hypoxic New Born
SA192015SW33_097Hypoxic New Born
SA192016WM501G-LAMB_062Hypoxic New Born
SA192017WM190-LAMB#1_059Hypoxic New Born
SA192018WM523LAMB1_060Hypoxic New Born
SA192019WM510G LAMB1_061Hypoxic New Born
SA192020WM476GLAMB2_063Hypoxic New Born
SA192021WM451W LAMB_064Hypoxic New Born
SA192022WJP4_024Hypoxic Non-preg
SA192023LZ11_011Hypoxic Non-preg
SA192024LZ13_013Hypoxic Non-preg
SA192025LZ14_014Hypoxic Non-preg
SA192026LZ12_012Hypoxic Non-preg
SA192027LZ15_015Hypoxic Non-preg
SA192028WJP21_107Hypoxic Non-preg
SA192029WJP3_023Hypoxic Non-preg
SA192030WJP5_025Hypoxic Non-preg
SA192031SW4_068Hypoxic Non-preg
SA192032SW34_098Hypoxic Non-preg
SA192033SW35_099Hypoxic Non-preg
SA192034SW3_067Hypoxic Non-preg
SA192035WJP1_021Hypoxic Non-preg
SA192036SW1_065Hypoxic Non-preg
SA192037SW2_066Hypoxic Non-preg
SA192038LZ20_020Hypoxic Preg
SA192039LZ19_019Hypoxic Preg
SA192040LZ17_017Hypoxic Preg
SA192041LZ16_016Hypoxic Preg
SA192042LZ18_018Hypoxic Preg
Showing results 1 to 94 of 94

Collection:

Collection ID:CO002118
Collection Summary:These samples were flash frozen in liquid nitrogen & stored at -80C
Sample Type:Adipose tissue

Treatment:

Treatment ID:TR002137
Treatment Summary:2, 3-6, Animals were housed at either low or high altitude. Uterine samples are from the adult ewe's while other samples are from either fetus, newborns, or adult animals.

Sample Preparation:

Sampleprep ID:SP002131
Sampleprep Summary:Extraction of Mammalian Tissue Samples: 1. References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ (in press) 2.Starting material: Liver sample: weigh 4mg per sample into 2mL Eppendorf tubes. 3. Equipment: Centrifuge (Eppendorf 5415 D) Calibrated pipettes 1-200μl and 100-1000μl Eppendorf tubes 2mL, clear (Cat. No. 022363204) Centrifuge tubes 50mL, polypropylene Eppendorff Tabletop Centrifuge (Proteomics core Lab.) ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer (VWR) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Turex mini homogenizer 4. Chemicals Acetonitrile, LCMS grade (JT Baker; Cat. No.9829-02) Isopropanol, HPLC grade (JT Baker; Cat. No. 9095-02) Methanol Acetone Crushed ice 18 MΩ pure water (Millipore) Nitrogen line with pipette tip pH paper 5-10 (EMD Chem. Inc.) 5. Procedure Preparation of extraction mix and material before experiment: Switch on bath to pre-cool at –20°C (±2°C validity temperature range) Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper Make the extraction solution by mixing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 De-gas the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization. The residue should contain membrane lipids because these are supposedly not soluble enough to be found in the 50% acetonitrile solution. Therefore, this ‘membrane residue’ is now taken for membrane lipidomic fingerprinting using the nanomate LTQ ion trap mass spectrometer. Likely, a good solvent to redissolve the membrane lipids is e.g. 75% isopropanol (degassed as given above). If the ‘analysis’ aliquot is to be used for semi lipophilic compounds such as tyrosine pathway intermediates (incl. dopamine, serotonine etc, i.e. polar aromatic compounds), then these are supposedly to be found together with the ‘GCTOF’ aliquot. We can assume that this mixture is still too complex for Agilent chipLCMS. Therefore, in order to develop and validate target analysis for such aromatic compounds, we should use some sort of Solid Phase purification. We re-suspend the dried ‘GCTOF’ aliquot in 300 l water (degassed as before) to take out sugars, aliphatic amino acids, hydroxyl acids and similar logP compounds. The residue should contain our target aromatics .We could also try to adjust pH by using low concentration acetate or phosphate buffer. The residue could then be taken up in 50% acetonitrile and used for GCTOF and Agilent chipMS experiments. The other aliquot should be checked how much of our target compounds would actually be found in the ‘sugar’ fraction. 6. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 7. Quality assurance For each sequence of sample extractions, perform one blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. 8. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules.

Combined analysis:

Analysis ID AN003324
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus IV GC
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um)
MS Type EI
MS instrument type QTOF
MS instrument name Leco Pegasus IV TOF
Ion Mode UNSPECIFIED
Units normalized peak height

Chromatography:

Chromatography ID:CH002463
Chromatography Summary:GC-TOF Method: Instruments: Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS Injector conditions: Agilent 6890 GC is equipped with a Gerstel automatic liner exchange system (ALEX) that includes a multipurpose sample (MPS2) dual rail, and a Gerstel CIS cold injection system (Gerstel, Muehlheim, Germany) with temperature program as follows: 50°C to 275°C final temperature at a rate of 12 °C/s and hold for 3 minutes. Injection volume is 0.5 μl with 10 μl/s injection speed on a splitless injector with purge time of 25 seconds. Liner (Gerstel #011711-010-00) is changed after every 10 samples, (using the Maestro1 Gerstel software vs. 1.1.4.18). Before and after each injection, the 10 μl injection syringe is washed three times with 10 μl ethyl acetate. Gas Chromatography conditions: A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min.
Instrument Name:Leco Pegasus IV GC
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC

MS:

MS ID:MS003094
Analysis ID:AN003324
Instrument Name:Leco Pegasus IV TOF
Instrument Type:QTOF
MS Type:EI
MS Comments:A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da.
Ion Mode:UNSPECIFIED
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