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MB Sample ID: SA045185
| Local Sample ID: | 1444592 |
| 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 |
Select appropriate tab below to view additional metadata details:
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:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 1444592 | SA045185 | FL009047 | db/db | Genotype |
| 1444592 | SA045185 | FL009047 | air | exposure |
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 During exposure, mice were placed within individual wire mesh cages and food and water were withdrawn.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 |
