Summary of Study ST001039

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 PR000679. The data can be accessed directly via it's Project DOI: 10.21228/M8X10M 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 IDST001039
Study TitleDenver Asthma Panel Study-CHEAR Ancillary Study (part II)
Study SummaryUrban environments remain a poorly understood toxic environment for children with asthma, where improved exposure characterization and estimation of exposurehealth outcome relationships are clearly needed. The goal of this project is to investigate the interactions between relevant environmental exposures and asthma severity in a year-long longitudinal study of urban children with asthma. Environmental and clinical samples are being collected at 3 seasonal visits. Using these samples, we will measure the effects of multiple relevant exposures (environmental tobacco smoke (ETS), polycyclic aromatic hydrocarbons (PAHs), phthalates, and volatile organic compounds (VOCs)) on biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids) and asthma outcomes. Our overall hypothesis is that relevant environmental exposures and their interactions drive disease severity in urban children with asthma. We will test this hypothesis by investigating the following aims: Aim 1: To investigate how environmental exposures (ETS, PAHs, phthalates, and VOCs) and their interactions contribute to asthma severity in urban children. Aim 2: To determine if environmental exposures in children with asthma are associated with changes in in biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids). Aim 3: To determine which biological responses mediate the relationships between environmental exposures and asthma severity. Aim 4: To compare environmental exposures and biological responses in asthmatic and non-asthmatic children
Institute
Emory University
DepartmentSchool of Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameUppal
First NameKaran
Address615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Emailkuppal2@emory.edu
Phone(404) 727 5027
Submit Date2018-07-12
Total Subjects169
Study CommentsBoth CHEAR pooled urine samples and Clinical Biomarker Laboratory pooled plasma samples were used
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2021-08-31
Release Version1
Karan Uppal Karan Uppal
https://dx.doi.org/10.21228/M8X10M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000679
Project DOI:doi: 10.21228/M8X10M
Project Title:Denver Asthma Panel Study-CHEAR Ancillary Study
Project Type:NIH/NIEHS 1U2CES026560-01
Project Summary:Urban environments remain a poorly understood toxic environment for children with asthma, where improved exposure characterization and estimation of exposurehealth outcome relationships are clearly needed. The goal of this project is to investigate the interactions between relevant environmental exposures and asthma severity in a year-long longitudinal study of urban children with asthma. Environmental and clinical samples are being collected at 3 seasonal visits. Using these samples, we will measure the effects of multiple relevant exposures (environmental tobacco smoke (ETS), polycyclic aromatic hydrocarbons (PAHs), phthalates, and volatile organic compounds (VOCs)) on biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids) and asthma outcomes. Our overall hypothesis is that relevant environmental exposures and their interactions drive disease severity in urban children with asthma. We will test this hypothesis by investigating the following aims: Aim 1: To investigate how environmental exposures (ETS, PAHs, phthalates, and VOCs) and their interactions contribute to asthma severity in urban children. Aim 2: To determine if environmental exposures in children with asthma are associated with changes in in biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids). Aim 3: To determine which biological responses mediate the relationships between environmental exposures and asthma severity. Aim 4: To compare environmental exposures and biological responses in asthmatic and non-asthmatic children
Institute:Emory University
Department:School of Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Uppal
First Name:Karan
Address:615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Email:kuppal2@emory.edu
Phone:(404) 727 5027
Funding Source:NIEHS ES026560
Contributors:Andrew Lui (University of Colorado Denver), Tasha Fingerlin ( University of Colorado Denver), Jonathon Thornburg (University of Colorado Denver), and Dean P. Jones (Emory University)

Subject:

Subject ID:SU001088
Subject Type:Urine samples
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Teens (12-17 yr)

Factors:

Subject type: Urine samples; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample.Matrix
SA070572Q-Std Plasma pool_4b_1Plasma
SA070573NIST SRM 1950_1bPlasma
SA070574NIST SRM 1950_1aPlasma
SA070575Q-Std Plasma pool_4a_1Plasma
SA070576Q-Std Plasma pool_3a_1Plasma
SA070577Q-Std Plasma pool_2a_1Plasma
SA070578Q-Std Plasma pool_2b_1Plasma
SA070579Q-Std Plasma pool_1a_2Plasma
SA070580Q-Std Plasma pool_3b_1Plasma
SA070581Q-Std Plasma pool_1b_2Plasma
SA070582Q-Std Plasma pool_4a_2Plasma
SA070583Q-Std Plasma pool_4b_2Plasma
SA070584NIST SRM 1950_2bPlasma
SA070585Q-Std Plasma pool_3b_2Plasma
SA070586Q-Std Plasma pool_3a_2Plasma
SA070587Q-Std Plasma pool_2a_2Plasma
SA070588Q-Std Plasma pool_2b_2Plasma
SA070589Q-Std Plasma pool_1b_1Plasma
SA070590NIST SRM 1950_2aPlasma
SA070591Q-Std Plasma pool_1a_1Plasma
SA070592chearurine_2c_2Urine
SA070593chearurine_2d_2Urine
SA070594C-1G2Q5-U-04_2Urine
SA070595C-1G4D1-U-03_2Urine
SA070596C-1G9T1-U-00_2Urine
SA070597C-1GB27-U-00_2Urine
SA070598C-1G660-U-02_2Urine
SA070599C-1G389-U-04_2Urine
SA070600C-1G2L6-U-03_2Urine
SA070601C-1G8D7-U-03_2Urine
SA070602C-1G3U5-U-01_2Urine
SA070603C-1GAL1-U-04_2Urine
SA070604C-1GB50-U-00_2Urine
SA070605C-1GA77-U-01_2Urine
SA070606C-1FXP1-U-02_2Urine
SA070607C-1G0T0-U-00_2Urine
SA070608C-1FY18-U-02_2Urine
SA070609C-1FZN3-U-00_2Urine
SA070610C-1G2V4-U-04_2Urine
SA070611C-1GAY2-U-00_2Urine
SA070612C-1G7Y2-U-04_2Urine
SA070613C-1G5Y4-U-00_2Urine
SA070614C-1G314-U-02_2Urine
SA070615C-1G8G1-U-04_2Urine
SA070616C-1G5M1-U-00_2Urine
SA070617chearurine_2f_2Urine
SA070618chearurine_2e_2Urine
SA070619C-1G322-U-03_2Urine
SA070620C-1G603-U-00_2Urine
SA070621C-1FXK2-U-00_1Urine
SA070622C-1GAM9-U-02_1Urine
SA070623C-1G5W9-U-01_2Urine
SA070624C-1G2K8-U-00_2Urine
SA070625chearurine_3b_2Urine
SA070626chearurine_3a_2Urine
SA070627C-1G1L7-U-00_2Urine
SA070628C-1FWY2-U-00_2Urine
SA070629C-1G1M5-U-02_2Urine
SA070630C-1G520-U-04_2Urine
SA070631C-1G4L4-U-02_2Urine
SA070632C-1G4U4-U-01_2Urine
SA070633C-1GB43-U-03_2Urine
SA070634C-1G2A0-U-03_2Urine
SA070635C-1FZH7-U-00_2Urine
SA070636C-1G5C3-U-02_2Urine
SA070637C-1G4Y5-U-00_2Urine
SA070638C-1FY26-U-04_2Urine
SA070639C-1G0U8-U-02_2Urine
SA070640C-1G3F8-U-00_2Urine
SA070641C-1FY42-U-01_2Urine
SA070642chearurine_1d_2Urine
SA070643chearurine_1c_2Urine
SA070644C-1G5U3-U-03_2Urine
SA070645C-1G1S1-U-02_2Urine
SA070646C-1G5X6-U-01_2Urine
SA070647C-1G2A0-U-04_2Urine
SA070648C-1G546-U-02_2Urine
SA070649C-1G3X8-U-00_2Urine
SA070650C-1G520-U-02_2Urine
SA070651C-1G2M4-U-00_2Urine
SA070652C-1G2Q5-U-00_2Urine
SA070653C-1G1K9-U-00_2Urine
SA070654C-1G082-U-00_2Urine
SA070655C-1G3H4-U-01_2Urine
SA070656C-1G918-U-01_2Urine
SA070657C-1FYV7-U-02_2Urine
SA070658C-1G7X4-U-01_2Urine
SA070659C-1G7V9-U-00_2Urine
SA070660C-1FXA4-U-04_2Urine
SA070661C-1FZE3-U-04_2Urine
SA070662C-1G7W7-U-03_2Urine
SA070663C-1FY42-U-03_2Urine
SA070664C-1G1T9-U-02_2Urine
SA070665C-1GAN6-U-00_1Urine
SA070666C-1GAS5-U-04_1Urine
SA070667chearurine_1f_2Urine
SA070668chearurine_1e_2Urine
SA070669chearurine_2a_2Urine
SA070670chearurine_2b_2Urine
SA070671C-1FZ33-U-01_2Urine
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Collection:

Collection ID:CO001082
Collection Summary:Urine samples were collected by random catch methods and transferred to 1.8 ml freezer tubes and stored in a -70 degree C freezer. The samples were shipped on dry ice to the metabolomics analysis lab at Emory University.
Sample Type:Urine
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001102
Treatment Summary:Samples were received frozen in aliquouts of <250uL. Prior to analysis, samples were thawed and prepared for HRM analysis using the standard protocols described in the Sample Preparation section.

Sample Preparation:

Sampleprep ID:SP001095
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, plasma aliquots were removed from storage at -80 degrees C and thawed on ice. Each cryotube was then vortexed briefly to ensure homogeneity, and 50 microliters was transferred to a clean microfuge tube. Immediately after, the plasma was treated with 100 microliters of ice-cold LC-MS grade acetonitrile (Sigma Aldrich) containing 2.5 microliters of internal standard solution with eight stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, urine was equilibrated for 30 min on ice, upon which precipitated proteins were removed by centrifuge (14,000 rpm at 4 degrees C for 10 min). The resulting supernatant (100 microliters) was removed, added to a low volume autosampler vial and maintained at 4 degrees C until analysis (<22 h).
Sampleprep Protocol ID:HRM_SP_082016_01
Sampleprep Protocol Filename:EmoryUniversity_HRM_SP_082016_01.pdf
Sampleprep Protocol Comments:Date effective: 30 July 2016
Extraction Method:2:1 acetonitrile: sample followed by vortexing and centrifugation

Combined analysis:

Analysis ID AN001712 AN001713
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters XBridge 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:CH001208
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:20160920_posHILIC120kres5min_ESI_c18negwash.meth
Chromatography Comments:Triplicate injections for each chromatography mode
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XBridge Amide (50 x 2.1mm,2.5um)
Column Temperature:60C
Flow Gradient:A= water, B= acetontrile, 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
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:CH001209
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 0.5 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:Thermo Dionex Ultimate 3000
Column Name:Thermo Higgins C18 (50 x 2.1mm,3um)
Column Temperature:60C
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
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:MS001584
Analysis ID:AN001712
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
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
Resolution Setting:120,000
Scanning Range:85-1275
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
  
MS ID:MS001585
Analysis ID:AN001713
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
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
Resolution Setting:120,000
Scanning Range:85-1275
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
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