Summary of Study ST002264

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 PR001446. The data can be accessed directly via it's Project DOI: 10.21228/M8T70R This work is supported by NIH grant, U2C- DK119886.

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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 IDST002264
Study TitleTranscriptomic-Metabolomic Profiling in Mouse Lung Tissues Reveals Sex- and Strain-Based Differences
Study SummaryThere has been a heighted interest in understanding the influences of sex and strain on variety of diseases states. We assessed the metabolomics profiles of male and female C57B6/J as well as male and female C3H/HeN. We pretreated each of these mice groups with 25mg/kg of Aurothioglucose (ATG) prior to being exposed to either 100% fitered air, or >95% oxygen for 96 hours. These studies begin to address the underlying altered metabolomic signaling that is influenced by sex and/or strain.
Institute
University of Oklahoma Health Sciences Center
DepartmentSection of Neonatal-Perinatal Medicine
LaboratoryClinical Biomarkers Laboratory
Last NameTipple
First NameTrent
Address1200 North Everett Drive, ETNP 7504 Oklahoma City, Oklahoma 73104-5407
EmailTrent-Tipple@ouhsc.edu
Phone405-271-5215
Submit Date2022-06-17
Total Subjects48
Study CommentsClinical Biomarker Laboratory pooled plasma samples were used as standards
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-08-30
Release Version1
Trent Tipple Trent Tipple
https://dx.doi.org/10.21228/M8T70R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001446
Project DOI:doi: 10.21228/M8T70R
Project Title:Transcriptomic-Metabolomic Profiling in Mouse Lung Tissues Reveals Sex- and Strain-Based Differences
Project Type:Sex- and Strain-Based Differences
Project Summary:There has been a heighted interest in understanding the influences of sex and strain on variety of diseases states. We assessed the metabolomics profiles of male and female C57B6/J as well as male and female C3H/HeN. We pretreated each of these mice groups with 25mg/kg of Aurothioglucose (ATG) prior to being exposed to either 100% fitered air, or >95% oxygen for 96 hours. These studies begin to address the underlying altered metabolomic signaling that is influenced by sex and/or strain.
Institute:Univeristy of Oklahoma Health Sciences Center
Department:Section of Neonatal-Perinatal Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Tipple
First Name:Trent
Address:1200 North Everett Drive, ETNP 7504 Oklahoma City, Oklahoma 73104-5407
Email:Trent-Tipple@ouhsc.edu
Phone:405-271-5215

Subject:

Subject ID:SU002350
Subject Type:mouse lungs
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:mice 6-8 weeks

Factors:

Subject type: mouse lungs; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id sample type Animal Sex Treatment1 Treatment2
SA21741324_1Mouse Lung Study Sample C3H/Hen Female ATG 95hr 100% O2
SA21741422_1Mouse Lung Study Sample C3H/Hen Female ATG 95hr 100% O2
SA21741523_1Mouse Lung Study Sample C3H/Hen Female ATG 95hr 100% O2
SA21741617_1Mouse Lung Study Sample C3H/Hen Female ATG Room Air
SA21741716_1Mouse Lung Study Sample C3H/Hen Female ATG Room Air
SA21741818_1Mouse Lung Study Sample C3H/Hen Female ATG Room Air
SA21741921_1Mouse Lung Study Sample C3H/Hen Female Saline 95hr 100% O2
SA21742020_1Mouse Lung Study Sample C3H/Hen Female Saline 95hr 100% O2
SA21742119_1Mouse Lung Study Sample C3H/Hen Female Saline 95hr 100% O2
SA21742213_1Mouse Lung Study Sample C3H/Hen Female Saline Room Air
SA21742314_1Mouse Lung Study Sample C3H/Hen Female Saline Room Air
SA21742415_1Mouse Lung Study Sample C3H/Hen Female Saline Room Air
SA21742512_1Mouse Lung Study Sample C3H/Hen Male ATG 95hr 100% O2
SA21742611_1Mouse Lung Study Sample C3H/Hen Male ATG 95hr 100% O2
SA21742710_1Mouse Lung Study Sample C3H/Hen Male ATG 95hr 100% O2
SA2174285_1Mouse Lung Study Sample C3H/Hen Male ATG Room Air
SA2174294_1Mouse Lung Study Sample C3H/Hen Male ATG Room Air
SA2174306_1Mouse Lung Study Sample C3H/Hen Male ATG Room Air
SA2174318_1Mouse Lung Study Sample C3H/Hen Male Saline 95hr 100% O2
SA2174327_1Mouse Lung Study Sample C3H/Hen Male Saline 95hr 100% O2
SA2174339_1Mouse Lung Study Sample C3H/Hen Male Saline 95hr 100% O2
SA2174343_1Mouse Lung Study Sample C3H/Hen Male Saline Room Air
SA2174351_1Mouse Lung Study Sample C3H/Hen Male Saline Room Air
SA2174362_1Mouse Lung Study Sample C3H/Hen Male Saline Room Air
SA21743734_1Mouse Lung Study Sample C57Bl6 Female ATG 95hr 100% O2
SA21743836_1Mouse Lung Study Sample C57Bl6 Female ATG 95hr 100% O2
SA21743935_1Mouse Lung Study Sample C57Bl6 Female ATG 95hr 100% O2
SA21744030_1Mouse Lung Study Sample C57Bl6 Female ATG Room Air
SA21744129_1Mouse Lung Study Sample C57Bl6 Female ATG Room Air
SA21744228_1Mouse Lung Study Sample C57Bl6 Female ATG Room Air
SA21744332_1Mouse Lung Study Sample C57Bl6 Female Saline 95hr 100% O2
SA21744433_1Mouse Lung Study Sample C57Bl6 Female Saline 95hr 100% O2
SA21744531_1Mouse Lung Study Sample C57Bl6 Female Saline 95hr 100% O2
SA21744626_1Mouse Lung Study Sample C57Bl6 Female Saline Room Air
SA21744725_1Mouse Lung Study Sample C57Bl6 Female Saline Room Air
SA21744827_1Mouse Lung Study Sample C57Bl6 Female Saline Room Air
SA21744947_1Mouse Lung Study Sample C57Bl6 Male ATG 95hr 100% O2
SA21745046_1Mouse Lung Study Sample C57Bl6 Male ATG 95hr 100% O2
SA21745148_1Mouse Lung Study Sample C57Bl6 Male ATG 95hr 100% O2
SA21745240_1Mouse Lung Study Sample C57Bl6 Male ATG Room Air
SA21745342_1Mouse Lung Study Sample C57Bl6 Male ATG Room Air
SA21745441_1Mouse Lung Study Sample C57Bl6 Male ATG Room Air
SA21745544_1Mouse Lung Study Sample C57Bl6 Male Saline 95hr 100% O2
SA21745645_1Mouse Lung Study Sample C57Bl6 Male Saline 95hr 100% O2
SA21745743_1Mouse Lung Study Sample C57Bl6 Male Saline 95hr 100% O2
SA21745839_1Mouse Lung Study Sample C57Bl6 Male Saline Room Air
SA21745937_1Mouse Lung Study Sample C57Bl6 Male Saline Room Air
SA21746038_1Mouse Lung Study Sample C57Bl6 Male Saline Room Air
SA217461q3June2014_1f_1plasma - - - -
SA217462nist2_1plasma - - - -
SA217463q3June2014_1e_1plasma - - - -
SA217464q3June2014_1d_1plasma - - - -
SA217465q3June2014_1a_1plasma - - - -
SA217466q3June2014_1b_1plasma - - - -
SA217467q3June2014_1c_1plasma - - - -
SA217468nist_1plasma - - - -
Showing results 1 to 56 of 56

Collection:

Collection ID:CO002343
Collection Summary:Animal studies were performed at the University of Alabama Birmingham using protocols approved by the Institutional Animal Care and Use Committee (IUCAC #20001). C57Bl/6 and C3H/HeN adult mice (6-8 weeks old) were purchased from Harlan (Indianapolis, IN). After acclimation, mice were euthanized and lung tissues snap-frozen and stored at -80C until needed.
Collection Protocol Filename:EmoryUniversity_HRM_SamplePreparation_tissue_062016_v1.pdf
Sample Type:mouse lungs
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR002362
Treatment Summary:Mice were exposed to either single IP injection +/- 25mg/kg ATG or saline prior to hyperoxia (>95 oxygen) or room air for 96 hours.

Sample Preparation:

Sampleprep ID:SP002356
Sampleprep Summary:Samples were prepared for metabolomics analysis using established methods (Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to analysis, lung samples were removed from storage at -80 degrees C and thawed on ice. The 20-30 mg of each lung tissue sample was then mixed with ice cold LC-MS grade acetonitrile: water mixture (Sigma-Aldrich; 2:1 ratio; 15uL per mg tissue) which contains 2.5uL per 100uL of internal standard solution with eight stable isotopic chemicals selected to cover a range of chemical properties. Samples are then sonicated on ice to ensure metabolite extraction as previously described (Chandler et al (2016) AJ Physiology; Hu et al. (2019) AJ Pathology). Following sonication, tissue lysates are then equilibrated for 30 mins on ice, upon which precipitated proteins are removed by centrifuge (16.1xg at 4C for 10 min). The resulting supernatant containing metabolite extract (100uL0 is removed, added to a low volume autosampler vial and maintained at 4C until analysis (<22h).
Sampleprep Protocol ID:HRM_SP_tissue_062016_v1
Sampleprep Protocol Filename:EmoryUniversity_HRM_SamplePreparation_tissue_062016_v1.pdf
Sampleprep Protocol Comments:Date effective: 30 July 2016
Processing Storage Conditions:On ice
Extraction Method:2:1 acetonitrile: sample followed by vortexing and centrifugation

Combined analysis:

Analysis ID AN003698 AN003699
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Dionex UltiMate 3000 Dionex UltiMate 3000
Column Waters XBridge BEH Amide XP HILIC (50 x 2.1mm x 2.5um) with Thermo Accucore HILIC guard Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Fusion Tribrid Orbitrap Thermo Fusion Tribrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002740
Chromatography Summary:The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 microliters of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C.
Methods ID:2% formic acid in LC-MS grade water
Methods Filename:EmoryUniversity_HRM_Fusion_chromatography_5min_092017_v1.pdf
Chromatography Comments:Triplicate injections for each chromatography mode
Instrument Name:Dionex UltiMate 3000
Column Name:Waters XBridge BEH Amide XP HILIC (50 x 2.1mm x 2.5um) with Thermo Accucore HILIC guard
Column Temperature:60C
Sample Injection:10 uL
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:100 uL
Chromatography Type:HILIC
  
Chromatography ID:CH002741
Chromatography Summary:The C18 column is operated parallel to the HILIC column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6- port switching valves. During operation of the C18 method, the MS is operated in negative ion mode and 10 uL of sample is injected onto the C18 column while the HILIC column is flushing with wash solution. Flow rate is maintained at 0.4 mL/min until 1.5 min, increased to 0.5 mL/min at 2 min and held for 3 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 10mM ammonium acetate in LC-MS grade water. Initial mobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min.
Methods ID:10mM ammonium acetate in LC-MS grade water
Methods Filename:20160920_negC18120kres5min_ESI_HILICposwash.meth
Instrument Name:Dionex UltiMate 3000
Column Name:Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005
Column Temperature:60C
Flow Rate:0.4 mL/min for 1.5 min; linear increase to 0.5 mL/min at 2 min held for 3 min
Sample Injection:10 uL
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:100 uL
Chromatography Type:Reversed phase

MS:

MS ID:MS003449
Analysis ID:AN003698
Instrument Name:Thermo Fusion Tribrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:apLCMS, xMSanalyzer, xMSannotator
Ion Mode:POSITIVE
Capillary Temperature:250C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:150C
Mass Accuracy:< 3ppm
Spray Voltage:3500
Activation Parameter:5.00E+05
Activation Time:118ms
Interface Voltage:S-Lens RF level= 55
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
  
MS ID:MS003450
Analysis ID:AN003699
Instrument Name:Thermo Fusion Tribrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:apLCMS, xMSanalyzer, xMSannotator
Ion Mode:NEGATIVE
Capillary Temperature:250C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:150C
Mass Accuracy:< 3ppm
Spray Voltage:-4000
Activation Parameter:5.00E+05
Activation Time:118ms
Interface Voltage:S-Lens RF level= 55
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
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