Summary of study ST000815

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 PR000580. The data can be accessed directly via it's Project DOI: 10.21228/M8PX0D This work is supported by NIH grant, U2C- DK119886.

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Study IDST000815
Study Titledb/db WT ozone and air exposed mice
Study SummaryThe goal of this study was to characterize the metabolic impact manifested in mouse lung following acute ozone exposure, comparing differential effects experienced by lean and obese model mice.
Institute
Harvard School of Public Health
Last NameMathews
First NameJoel
Address1 DNA Way
Emailjoel.mathews@gmail.com
Phone3019283058
Submit Date2017-06-05
Analysis Type DetailGC/LC-MS
Release Date2017-10-11
Release Version1
Joel Mathews Joel Mathews
https://dx.doi.org/10.21228/M8PX0D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000580
Project DOI:doi: 10.21228/M8PX0D
Project Title:db/db WT ozone and air exposed mice
Project Summary:The goal of this study was to characterize the metabolic impact manifested in mouse lung following acute ozone exposure, comparing differential effects experienced by lean and obese model mice.
Institute:Harvard School of Public Health
Last Name:Mathews
First Name:Joel
Address:1 DNA Way, South San Francisco, CA, 94080, USA
Email:joel.mathews@gmail.com
Phone:6504671824

Subject:

Subject ID:SU000841
Subject Type:db/db mouse and WT
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:10 weeks
Gender:female
Species Group:Mammal

Factors:

Subject type: db/db mouse and WT; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype exposure
SA0451781444589db/db air
SA0451791444588db/db air
SA0451801444587db/db air
SA0451811444590db/db air
SA0451821444591db/db air
SA0451831444586db/db air
SA0451841444593db/db air
SA0451851444592db/db air
SA0451861444598db/db ozone
SA0451871444597db/db ozone
SA0451881444596db/db ozone
SA0451891444599db/db ozone
SA0451901444601db/db ozone
SA0451911444594db/db ozone
SA0451921444595db/db ozone
SA0451931444600db/db ozone
SA0451621444605WT air
SA0451631444604WT air
SA0451641444606WT air
SA0451651444608WT air
SA0451661444609WT air
SA0451671444603WT air
SA0451681444607WT air
SA0451691444602WT air
SA0451701444612WT ozone
SA0451711444611WT ozone
SA0451721444610WT ozone
SA0451731444613WT ozone
SA0451741444614WT ozone
SA0451751444616WT ozone
SA0451761444617WT ozone
SA0451771444615WT ozone
Showing results 1 to 32 of 32

Collection:

Collection ID:CO000835
Collection Summary:Metabolon received 32 mouse lung samples on January 8, 2012. Following receipt, samples were inventoried, and immediately stored at -80oC. At the time of analysis samples were extracted and prepared for analysis using Metabolon’s standard solvent extraction method. The extracted samples were split into equal parts for analysis on the GC/MS and LC/MS/MS platforms. Also included were several technical replicate samples created from a homogeneous pool containing a small amount of all study samples (“Client Matrix”). General platform methods are described in APPENDIX A.
Sample Type:Lung

Treatment:

Treatment ID:TR000855
Treatment Summary:Female db/db mice on a C57BL/6 background and age- and sex-matched wildtype (WT) C57BL/6J mice were purchased from The Jackson Labs at age 6 weeks, allowed to acclimatize within the mouse vivarium at the Harvard T.H. Chan School of Public Health for 4 weeks, and studied at 10 weeks of age. db/db and WT mice were exposed for 3 hours to room air or to O3 (2 ppm) in stainless steel and plexiglass exposure chambers {Shore, 2003 #480}. During exposure, mice were placed within individual wire mesh cages and food and water were withdrawn. Mice were returned to their home cages immediately after exposure at which time food and water were restored. Mice were euthanized with an overdose of sodium pentobarbital 24 hours after cessation of exposure. For mice in the metabolomics study, after euthanasia, blood was obtained by cardiac puncture for the preparation of serum. The chest wall was then opened and a small incision was made in the left ventricle. 10 ml of ice cold PBS was gradually injected into the right ventricle in order to flush blood from the lungs. The lungs were then flash frozen in liquid nitrogen and stored at -80oC until shipped on dry ice to Metabolon Inc. (Durham, NC). Upon receipt, the lungs were again frozen at -80oC until analysis.

Sample Preparation:

Sampleprep ID:SP000848
Sampleprep Summary:The automated MicroLab STAR® system from Hamilton Company was used to prepare samples for metabolomics profiling. Equal weight of lungs was used from each mouse. Prior to the first step in the extraction process, recovery standards were added for quality control (QC) purposes. A series of organic and aqueous extractions proprietary to Metabolon Inc. was then used to remove protein while allowing maximum recovery of small molecules. Extracts were divided into two fractions. One was used for analysis by liquid chromatography (LC) and the other was used for analysis by gas chromatography (GC). Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent, frozen, and dried under vacuum. Samples were then prepared for the appropriate instrument, either LC/MS (mass spectrometry) or GC/MS, as described by Evans et al {Evans, 2009 #5074}. For a brief description of the methods used for LC/MS and GC/MS, see the online supplement. After analysis, raw data were extracted, peak-identified and QC processed using Metabolon's proprietary hardware and software. At the time of this analysis, identification of known chemical entities was based on comparison to metabolomic libraries of more than 1000 commercially available purified standard compounds. The combination of chromatographic properties and mass spectra gave an indication of a match to the specific compound or an isobaric entity.

Combined analysis:

Analysis ID AN001290 AN001291 AN001292
Analysis type MS MS MS
Chromatography type GC GC GC
Chromatography system Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer
Column 5% phenyl and the temperature ramp is from 40° to 300° C in a 16 minute period 5% phenyl and the temperature ramp is from 40° to 300° C in a 16 minute period 5% phenyl and the temperature ramp is from 40° to 300° C in a 16 minute period
MS Type EI ESI ESI
MS instrument type Single quadrupole Not supplied Not supplied
MS instrument name Thermo LTQ Thermo LTQ Thermo LTQ
Ion Mode POSITIVE POSITIVE NEGATIVE
Units total ion counts total ion counts total ion counts

Chromatography:

Chromatography ID:CH000905
Instrument Name:Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer
Column Name:5% phenyl and the temperature ramp is from 40° to 300° C in a 16 minute period
Chromatography Type:GC

MS:

MS ID:MS001183
Analysis ID:AN001290
Instrument Name:Thermo LTQ
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
  
MS ID:MS001184
Analysis ID:AN001291
Instrument Name:Thermo LTQ
Instrument Type:Not supplied
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001185
Analysis ID:AN001292
Instrument Name:Thermo LTQ
Instrument Type:Not supplied
MS Type:ESI
Ion Mode:NEGATIVE
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