Summary of study ST001428

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 PR000980. The data can be accessed directly via it's Project DOI: 10.21228/M8169P 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 IDST001428
Study TitleRole of environmental toxicants in modulating disease severity in children with NAFLD
Study SummaryThis project aims to further understand about how the environment impacts nonalcoholic fatty liver disease NAFLD and nonalcoholic steatohepatitis (NASH) in children. At present the NASH CRN has the largest, well characterized cohort of children with NAFLD, including clinical data, labs, cytokines, genetic polymorphisms, but no proteomics, metabolomics, lipidomics or toxicant assessment. Exposure and untargeted metabolomics analyses will examine the role of environmental toxicants in modulating disease severity and the endogenous response to exposures in children with NAFLD.
Institute
Emory University
DepartmentSchool of Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameTran
First NameViLinh
Address615 Michael St, suite 225, Atlanta GA 30322
Emailvtran6@emory.edu
Phone9122281788
Submit Date2020-07-17
Total Subjects427
Study CommentsBoth CHEAR pooled plasma samples and Clinical Biomarker Laboratory pooled plasma samples were used
Raw Data AvailableYes
Raw Data File Type(s).raw
Chear Study2017-1593
Analysis Type DetailLC-MS
Release Date2020-07-30
Release Version1
ViLinh Tran ViLinh Tran
https://dx.doi.org/10.21228/M8169P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000980
Project DOI:doi: 10.21228/M8169P
Project Title:Role of environmental toxicants in modulating disease severity in children with NAFLD
Project Type:NIH/NIEHS 1U2CES026560-01
Project Summary:This project aims to further understand about how the environment impacts nonalcoholic fatty liver disease NAFLD and nonalcoholic steatohepatitis (NASH) in children. At present the NASH CRN has the largest, well characterized cohort of children with NAFLD, including clinical data, labs, cytokines, genetic polymorphisms, but no proteomics, metabolomics, lipidomics or toxicant assessment. Exposure and untargeted metabolomics analyses will examine the role of environmental toxicants in modulating disease severity and the endogenous response to exposures in children with NAFLD.
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
Email:vtran6@emory.edu
Phone:9122281788
Funding Source:NIEHS ES026560

Subject:

Subject ID:SU001502
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:ages 2 to 18 years

Factors:

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

mb_sample_id local_sample_id Sample type
SA120602chearplasma_6c_2plasma
SA120603chearplasma_1f_2plasma
SA120604chearplasma_1e_2plasma
SA120605chearplasma_6d_2plasma
SA120606chearplasma_1d_2plasma
SA120607chearplasma_5e_2plasma
SA120608chearplasma_1b_2plasma
SA120609chearplasma_5f_2plasma
SA120610q3June2014_5b_2plasma
SA120611q3June2014_6a_2plasma
SA120612chearplasma_1a_2plasma
SA120613chearplasma_11c_2plasma
SA120614q3June2014_1a_2plasma
SA120615nist2_2plasma
SA120616q3June2014_11b_2plasma
SA120617chearplasma_11d_2plasma
SA120618chearplasma_6a_2plasma
SA120619chearplasma_6b_2plasma
SA120620q3June2014_11a_2plasma
SA120621q3June2014_10b_2plasma
SA120622chearplasma_10f_2plasma
SA120623chearplasma_10e_2plasma
SA120624chearplasma_11a_2plasma
SA120625chearplasma_11b_2plasma
SA120626chearplasma_5d_2plasma
SA120627chearplasma_1c_2plasma
SA120628q3June2014_1b_2plasma
SA120629chearplasma_5c_2plasma
SA120630nist1_2plasma
SA120631q3June2014_9b_2plasma
SA120632q3June2014_9a_2plasma
SA120633chearplasma_9a_2plasma
SA120634q3June2014_8b_2plasma
SA120635chearplasma_8f_2plasma
SA120636chearplasma_3c_2plasma
SA120637chearplasma_8e_2plasma
SA120638chearplasma_9b_2plasma
SA120639chearplasma_3b_2plasma
SA120640chearplasma_2f_2plasma
SA120641chearplasma_2e_2plasma
SA120642q3June2014_2b_2plasma
SA120643q3June2014_3a_2plasma
SA120644chearplasma_3a_2plasma
SA120645chearplasma_3d_2plasma
SA120646chearplasma_7e_2plasma
SA120647chearplasma_4a_2plasma
SA120648chearplasma_4b_2plasma
SA120649q3June2014_4a_2plasma
SA120650q3June2014_3b_2plasma
SA120651chearplasma_3e_2plasma
SA120652chearplasma_3f_2plasma
SA120653chearplasma_8c_2plasma
SA120654chearplasma_8d_2plasma
SA120655q3June2014_7b_2plasma
SA120656chearplasma_7f_2plasma
SA120657q3June2014_8a_2plasma
SA120658chearplasma_8a_2plasma
SA120659chearplasma_8b_2plasma
SA120660chearplasma_7d_2plasma
SA120661chearplasma_7c_2plasma
SA120662chearplasma_4f_2plasma
SA120663q3June2014_4b_2plasma
SA120664chearplasma_4e_2plasma
SA120665chearplasma_6e_2plasma
SA120666q3June2014_6b_2plasma
SA120667chearplasma_6f_2plasma
SA120668q3June2014_5a_2plasma
SA120669chearplasma_5a_2plasma
SA120670q3June2014_2a_2plasma
SA120671chearplasma_10c_2plasma
SA120672chearplasma_2a_2plasma
SA120673chearplasma_2b_2plasma
SA120674chearplasma_5b_2plasma
SA120675q3June2014_7a_2plasma
SA120676chearplasma_10b_2plasma
SA120677chearplasma_9d_2plasma
SA120678chearplasma_2d_2plasma
SA120679chearplasma_9c_2plasma
SA120680chearplasma_4d_2plasma
SA120681chearplasma_4c_2plasma
SA120682chearplasma_2c_2plasma
SA120683chearplasma_7b_2plasma
SA120684q3June2014_10a_2plasma
SA120685chearplasma_10a_2plasma
SA120686chearplasma_9f_2plasma
SA120687chearplasma_9e_2plasma
SA120688chearplasma_7a_2plasma
SA120689chearplasma_10d_2plasma
SA120176C-1ZNB8-S-01_002Serum
SA120177C-1ZND3-S-01_002Serum
SA120178C-20198-S-01_002Serum
SA120179C-1ZZF7-S-01_002Serum
SA120180C-1ZZD1-S-01_002Serum
SA120181C-1ZZG5-S-01_002Serum
SA120182C-20180-S-01_002Serum
SA120183C-201C6-S-01_002Serum
SA120184C-1ZSV9-S-01_002Serum
SA120185C-201D3-S-01_002Serum
SA120186C-20172-S-01_002Serum
SA120187C-201A0-S-01_002Serum
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Collection:

Collection ID:CO001497
Collection Summary:Serum obtained from blood vein draw for children, which are acquired near in time to liver biopsy, for the subject in the NASH CRN cohort. Blood samples were collected in red top vacutainer tubers and sit upright for 30 minutes for clot formation, followed by centrifugation and removal of 500uL aliquots of serum to 1.8mL freezer tubes and stores in a -70C freezer. The samples were shipped on dry ice from the clinical centers to CHEAR URR at Emory University.
Sample Type:Blood (serum)
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001517
Treatment Summary:Samples were received frozen in aliquouts of <250uL. Freeze-thaw history for study samples prior to receipt by the Emory URR is provided in the Study Design section. Prior to analysis, samples were thawed and prepared for HRM analysis using the standard protocols in the Sample Preparation section.

Sample Preparation:

Sampleprep ID:SP001510
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 AN002387 AN002388
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Dionex UltiMate 3000 Dionex UltiMate 3000
Column Waters XBridge BEH Amide XP HILIC ( 2.1mm x 50mm x 2.5um) with Thermo Accucore HILIC guard column Higgins endcapped C18 stainless steel column. (2.1mm x 50mm x 3μm) with Thermo Accucore HILIC guard column
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:CH001754
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:20200407_posHILIC120kres5min_ESI_c18negwash.meth
Chromatography Comments:Triplicate injections for each chromatography mode. Waters XBridge BEH Amide XP HILIC ( 2.1mm x 50mm x 2.5um) with Thermo Accucore HILIC guard column
Instrument Name:Dionex UltiMate 3000
Column Name:Waters XBridge BEH Amide XP HILIC ( 2.1mm x 50mm x 2.5um) with Thermo Accucore HILIC guard column
Column Temperature:60C
Sample Injection:10 uL
Solvent A:LC-MS grade water
Solvent B:LC-MS grade acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:100 uL
Chromatography Type:HILIC
  
Chromatography ID:CH001755
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:20200407_negC18120kres5min_ESI_HILICposwash.meth
Chromatography Comments:Higgins endcapped C18 stainless steel column. (2.1mm x 50mm x 3μm) with Thermo Accucore HILIC guard column. Product #TS-0521-C183; Thermo Accucore C18 guard column with holder, Product #17126-014005
Instrument Name:Dionex UltiMate 3000
Column Name:Higgins endcapped C18 stainless steel column. (2.1mm x 50mm x 3μm) with Thermo Accucore HILIC guard column
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:LC-MS grade water
Solvent B:LC-MS grade acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:100 uL
Chromatography Type:Reversed phase

MS:

MS ID:MS002229
Analysis ID:AN002387
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:none
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
  
MS ID:MS002230
Analysis ID:AN002388
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:none
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
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