Summary of Study ST002721
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 PR001687. The data can be accessed directly via it's Project DOI: 10.21228/M8NB07 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.
| Study ID | ST002721 |
| Study Title | Repeated Exposure to Wood Smoke Alters Pulmonary Gene and Metabolic Profiles |
| Study Summary | This project aims to evaluate the association of eucalyptus wood smoke exposure with perturbations to lung metabolism in a pre-clinical rat model. This cross-sectional study of male Long-Evans rats were exposed whole body to eucalyptus smoke for 4 consecutive days on week 1, followed by a 3-day break, and 3 subsequent days of smoke exposure on week 2. The smoke exposures were set to a target CO of 10ppm for the low smoke group and 20ppm for the high smoke group. Animal were sacrificed and lungs were extracted for metabolomics analysis. Exposures to eucalyptus smoke and biological perturbations to lung metabolism will be associated with known metabolic dysregulation associated with smoke exposures. |
| Institute | Emory University |
| Department | School of Medicine |
| Laboratory | Clinical Biomarkers Laboratory |
| Last Name | Tran |
| First Name | ViLinh |
| Address | 615 Michael St, Suite 225, Atlanta, GA 30322, USA |
| vtran6@emory.edu | |
| Phone | 4047275091 |
| Submit Date | 2023-05-12 |
| Num Groups | 3 |
| Total Subjects | 8 |
| Num Males | 8 |
| Study Comments | Clinical Biomarker Laboratory pooled plasma samples were used |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-05-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001687 |
| Project DOI: | doi: 10.21228/M8NB07 |
| Project Title: | Repeated Exposure to Wood Smoke Alters Pulmonary Gene and Metabolic Profiles |
| Project Summary: | This project aims to evaluate the association of eucalyptus wood smoke exposure with perturbations to lung metabolism in a pre-clinical rat model. This cross-sectional study of male Long-Evans rats were exposed whole body to eucalyptus smoke for 4 consecutive days on week 1, followed by a 3-day break, and 3 subsequent days of smoke exposure on week 2. The smoke exposures were set to a target CO of 10ppm for the low smoke group and 20ppm for the high smoke group. Animal were sacrificed and lungs were extracted for metabolomics analysis. Exposures to eucalyptus smoke and biological perturbations to lung metabolism will be associated with known metabolic dysregulation associated with smoke exposures. |
| Institute: | Emory University |
| Department: | School of Medicine |
| Laboratory: | Clinical Biomarkers Laboratory |
| Last Name: | Tran |
| First Name: | ViLinh |
| Address: | 615 Michael St, Suite 225, Atlanta, GA 30322, USA |
| Email: | vtran6@emory.edu |
| Phone: | 404-727-5091 |
| Contributors: | Matthew R. Smith, PdD, Collette M. Miller, PhD, Kymberly M. Gowdy, PhD, Dean P. Jones, PhD |
Subject:
| Subject ID: | SU002827 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Age Or Age Range: | 12 weeks |
| Gender: | Male |
Factors:
Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Class |
|---|---|---|
| SA273814 | 47_1 | 15 |
| SA273815 | 42_1 | 15 |
| SA273816 | 48_1 | 15 |
| SA273817 | 46_1 | 15 |
| SA273818 | 44_1 | 15 |
| SA273819 | 45_1 | 15 |
| SA273820 | 41_1 | 15 |
| SA273821 | 43_1 | 15 |
| SA273806 | 25_1 | 7.5 |
| SA273807 | 32_1 | 7.5 |
| SA273808 | 27_1 | 7.5 |
| SA273809 | 30_1 | 7.5 |
| SA273810 | 28_1 | 7.5 |
| SA273811 | 26_1 | 7.5 |
| SA273812 | 29_1 | 7.5 |
| SA273813 | 31_1 | 7.5 |
| SA273822 | 14_1 | Air |
| SA273823 | 9_1 | Air |
| SA273824 | 11_1 | Air |
| SA273825 | 15_1 | Air |
| SA273826 | 10_1 | Air |
| SA273827 | 13_1 | Air |
| SA273828 | 12_1 | Air |
| SA273829 | 16_1 | Air |
| SA273830 | q3June2014_1f_1 | NA |
| SA273831 | nist2_1 | NA |
| SA273832 | q3June2014_1e_1 | NA |
| SA273833 | q3June2014_1a_1 | NA |
| SA273834 | q3June2014_1c_1 | NA |
| SA273835 | nist1_1 | NA |
| SA273836 | q3June2014_1d_1 | NA |
| SA273837 | q3June2014_1b_1 | NA |
| Showing results 1 to 32 of 32 |
Collection:
| Collection ID: | CO002820 |
| Collection Summary: | The intact left lung was removed, and a longitudinal section was made to produce tissue samples for downstream metabolomic assessments. Lung section were frozen in liquid nitrogen and stored at -80°C until use. The samples were shipped on dry ice from the clinical centers to the Clinical Biomarkers Laboratory at Emory University. |
| Sample Type: | Lung |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002836 |
| Treatment Summary: | Samples were received frozen in aliquots of lung tissue. Prior to analysis, samples were thawed and prepared for HRM analysis using the standard protocols described in the Sample Preparation section. Eucalyptus was selected as the biomass of interest due to its prevalence and likeness of chaparral ecosystems present in Southern California and Australia, areas that have experienced growing severity of wildland fires in recent years. To mimic the deployment of common fire line shifts, rats were exposed to whole-body eucalyptus smoke over the course of two weeks. Exposure occurred for 4 consecutive days on week 1, followed by a 3-day break, and 3 subsequent days of smoke exposure on week 2. An n = 24 rats were randomized by weight into three groups based on body weight (n = 8 / group): filtered air, low smoke, and high smoke concentrations. The smoke exposures were set to a target CO of 10 ppm for the low smoke group and 20 ppm for the high smoke group. These concentrations bracket the National Wildfire Coordinating Group’s recommended exposure limit of 15 ppm, which is lower than the 35 ppm limit set by the National Institute for Occupational Safety and Health. Further, these concentrations were selected to avoid respiratory suppression and the potential for anti-inflammatory signaling from high concentrations of CO in the rodent. Eucalyptus smoke was generated in a quartz-tube furnace system set to a smoldering condition (~ 500°C) with a primary air flow at ~ 2 L/min. Additional details on the design of the tube furnace system can be found in Kim, et al. Generated smoke was diluted using a secondary air flow to maintain our target CO concentrations and was subsequently delivered to a whole-body inhalation chamber. CO and CO2 were continuously monitored using a nondispersive infrared analyzer (602 CO/CO2; CAI, Inc.) and nitrogen oxides were monitored using a chemiluminescent analyzer (42i NO/NO2/NOx; ThermoScientific). Environmental conditions in the chambers were measured in real-time using Dasylab Software (v.13.0; National Instruments). Particle size distribution within the exposure chamber was measured for 5 minutes at the mid-point of the exposure using an electrical low-pressure impactor (ELPI model 97-2E; Dekati Ltd.) and analyzed for surface area-weighted distributions (ELPIvi v.3.0; Dekati Ltd.). Final PM concentrations following each exposure was determined by gravimetrically weighing a glass-fiber filtered placed in the exhaust line of the quartz-tube furnace system before and after the combustion. Due to staffing limitations, VOCs were not able to be characterized for the specific exposures within this study. However, the chemicals found in eucalyptus smoke and concentration ranges generated in our tube furnace system can be found in Kim, et al. (36) and Kim, et al. Attributable to the length of the quartz tube used in our system, each daily exposure was limited to 1 hour. |
Sample Preparation:
| Sampleprep ID: | SP002833 |
| 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 20-30mg of each lung tissue samples was then mixed with ice cold LC-MS grade acetonitrile: water mixture (Sigma-Aldrich; 2:1 ration; 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 mins). The resulting supernatant containing metabolite extract (100uL) is removed, added to a low volume autosampler vial and maintained at 4C until analysis (<22h). |
| Sampleprep Protocol Filename: | EmoryUniversity_HRM_SamplePreparation_tissue_062016_v1.pdf |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004411 | AN004412 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters XBridge BEH Amide (50 x 2.1mm,2.5um) | Thermo Higgins C18 (50 x 2.1mm,3um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH003310 |
| 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 Filename: | EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf |
| Chromatography Comments: | Triplicate injections for each chromatography mode |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters XBridge BEH Amide (50 x 2.1mm,2.5um) |
| Column Temperature: | 60 |
| Flow Gradient: | A= water, B= acetonitrile, C= 2% formic acid in water; 22.5% A, 75% B, 2.5% C hold for 1.5 min, linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min |
| Flow Rate: | 0.35 mL/min for 1.5 min; linear increase to 0.4 mL/min at 4 min, hold for 1 min |
| Solvent A: | 100% water |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
| Solvent C: | 100% water; 2% formic acid |
| Chromatography ID: | CH003311 |
| 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 μL 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 0.5mL/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 Filename: | EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf |
| Chromatography Comments: | Triplicate injections for each chromatography mode |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Thermo Higgins C18 (50 x 2.1mm,3um) |
| Column Temperature: | 60 |
| Flow Gradient: | A= water, B= acetontrile, C= 10mM ammonium acetate in water; 60% A, 35% B, 5% C hold for 0.5 min, linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3 min |
| Flow Rate: | 0.4 mL/min for 1.5 min; linear increase to 0.5 mL/min at 2 min held for 3 min |
| Solvent A: | 100% water |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
| Solvent C: | 100% water; 10mM ammonium acetate |
MS:
| MS ID: | MS004158 |
| Analysis ID: | AN004411 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Xcalibur 3.0.63 |
| 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_DataAnalysis-MS_092017_v1.pdf |
| MS ID: | MS004159 |
| Analysis ID: | AN004412 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Xcalibur 3.0.63 |
| 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_DataAnalysis-MS_092017_v1.pdf |
