Summary of Study ST002501

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 PR001615. The data can be accessed directly via it's Project DOI: 10.21228/M8Z12P 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 IDST002501
Study TitleThe ECHO Cohort Exposome: First Steps using HHEAR Analysis – An Opportunity for ALL ECHO Cohorts to Contribute Type A Samples – Untargeted Analysis (ReCHARGE Cohort)
Study TypeCase-Control Study
Study SummaryThe ReCHARGE study is a case control study of children with Autism Spectrum Disorder, Developmental Delay, and who are typically developing. They were initially recruited into the study between the ages and 2 and 5 years of age, and are being seen again during middle childhood and adolescence. This research was supported by the Environmental influences on Child Health Outcomes (ECHO) program, Office of The Director, National Institutes of Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. ReCHARGE is an ECHO cohort which is supported by the following ECHO Program Collaborators: ECHO Coordinating Center: Duke Clinical Research Institute, Durham, North Carolina: Smith PB, Newby KL, Benjamin DK; U2C OD023375 ECHO Data Analysis Center: Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland: Jacobson LP; Research Triangle Institute, Durham, North Carolina: Catellier D; U24 OD023382 North Carolina Human Health Exposure Analysis Resource Hub: Research Triangle Institute: Fennell T, University of North Carolina at Chapel Hill: Sumner S, University of North Carolina at Charlotte: Du X; U2C ES030857 Human Health Exposure Analysis Resource Coordinating Center: Westat, Inc., Rockville, Maryland: O’Brien B; U24 ES026539
Institute
University of California, Davis
DepartmentSchool of Medicine, Public Health Sciences
Last NameDeborah
First NameBennett
AddressPublic Health Sciences Medical Sciences 1-C Davis, CA 95616
Emaildhbennett@ucdavis.edu
Phone(530) 754-8282
Submit Date2023-03-01
Total Subjects213
Study CommentsHHEAR Project EM20-0011, ECHO Project EC0376
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2024-03-01
Release Version1
Bennett Deborah Bennett Deborah
https://dx.doi.org/10.21228/M8Z12P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001615
Project DOI:doi: 10.21228/M8Z12P
Project Title:The ECHO Cohort Exposome: First Steps using HHEAR Analysis – An Opportunity for ALL ECHO Cohorts to Contribute Type A Samples – Untargeted Analysis (ReCHARGE Cohort)
Project Type:C18 Reversed-Phase Broad Spectrum Metabolomics
Project Summary:This project was funded by the NIH Environmental influences on Child Health Outcomes (ECHO) Program. Untargeted metabolomics profiling data was acquired from urine samples provided by 14 ECHO cohorts.
Institute:NC HHEAR Hub
Department:Untargeted Analysis
Laboratory:Sumner Lab
Last Name:Rushing
First Name:Blake
Address:Nutrition Research Institute, UNC-CH, 500 Laureate Way, Kannapolis, NC 28081
Email:blake_rushing@unc.edu
Phone:(704) 282-9838
Funding Source:This research was supported by the Environmental influences on Child Health Outcomes (ECHO) program, Office of The Director, National Institutes of Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The ReCHARGE ECHO Cohort is supported by the following ECHO Program Collaborators: ECHO Coordinating Center: Duke Clinical Research Institute, Durham, North Carolina: Smith PB, Newby KL, Benjamin DK; U2C OD023375; ECHO Data Analysis Center: Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland: Jacobson LP; Research Triangle Institute, Durham, North Carolina: Catellier D; U24 OD023382; North Carolina Human Health Exposure Analysis Resource Hub: Research Triangle Institute: Fennell T, University of North Carolina at Chapel Hill: Sumner S, University of North Carolina at Charlotte: Du X; U2C ES030857; Human Health Exposure Analysis Resource Coordinating Center: Westat, Inc., Rockville, Maryland: O’Brien B; U24 ES026539

Subject:

Subject ID:SU002598
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Sample Type Batch
SA250616ReCHARGE_B_8Blank 1
SA250617ReCHARGE_B_1Blank 1
SA250618ReCHARGE_B_7Blank 1
SA250619ReCHARGE_B_6Blank 1
SA250620ReCHARGE_B_2Blank 1
SA250621ReCHARGE_B_4Blank 1
SA250622ReCHARGE_B_3Blank 1
SA250623ReCHARGE_B_5Blank 1
SA250624ReCHARGE_B_14Blank 2
SA250625ReCHARGE_B_15Blank 2
SA250626ReCHARGE_B_13Blank 2
SA250627ReCHARGE_B_16Blank 2
SA250628ReCHARGE_B_12Blank 2
SA250629ReCHARGE_B_10Blank 2
SA250630ReCHARGE_B_9Blank 2
SA250631ReCHARGE_B_11Blank 2
SA250632ReCHARGE_B_22Blank 3
SA250633ReCHARGE_B_21Blank 3
SA250634ReCHARGE_B_19Blank 3
SA250635ReCHARGE_B_20Blank 3
SA250636ReCHARGE_B_18Blank 3
SA250637ReCHARGE_CHEAR_U_4CHEAR Urine Pool 1
SA250638ReCHARGE_CHEAR_U_1CHEAR Urine Pool 1
SA250639ReCHARGE_CHEAR_U_3CHEAR Urine Pool 1
SA250640ReCHARGE_CHEAR_U_2CHEAR Urine Pool 1
SA250641ReCHARGE_CHEAR_U_8CHEAR Urine Pool 2
SA250642ReCHARGE_CHEAR_U_7CHEAR Urine Pool 2
SA250643ReCHARGE_CHEAR_U_6CHEAR Urine Pool 2
SA250644ReCHARGE_CHEAR_U_5CHEAR Urine Pool 2
SA250645ReCHARGE_CHEAR_U_11CHEAR Urine Pool 3
SA250646ReCHARGE_CHEAR_U_10CHEAR Urine Pool 3
SA250647ReCHARGE_CHEAR_U_9CHEAR Urine Pool 3
SA250648ReCHARGE_HHEAR_U1_1HHEAR Urine Pool 1 (HHEAR_U1_20) 1
SA250649ReCHARGE_HHEAR_U1_4HHEAR Urine Pool 1 (HHEAR_U1_20) 1
SA250650ReCHARGE_HHEAR_U1_3HHEAR Urine Pool 1 (HHEAR_U1_20) 1
SA250651ReCHARGE_HHEAR_U1_2HHEAR Urine Pool 1 (HHEAR_U1_20) 1
SA250652ReCHARGE_HHEAR_U1_8HHEAR Urine Pool 1 (HHEAR_U1_20) 2
SA250653ReCHARGE_HHEAR_U1_7HHEAR Urine Pool 1 (HHEAR_U1_20) 2
SA250654ReCHARGE_HHEAR_U1_6HHEAR Urine Pool 1 (HHEAR_U1_20) 2
SA250655ReCHARGE_HHEAR_U1_5HHEAR Urine Pool 1 (HHEAR_U1_20) 2
SA250656ReCHARGE_HHEAR_U1_11HHEAR Urine Pool 1 (HHEAR_U1_20) 3
SA250657ReCHARGE_HHEAR_U1_10HHEAR Urine Pool 1 (HHEAR_U1_20) 3
SA250658ReCHARGE_HHEAR_U1_9HHEAR Urine Pool 1 (HHEAR_U1_20) 3
SA250659ReCHARGE_HHEAR_U2_3HHEAR Urine Pool 2 (HHEAR_U2_50) 1
SA250660ReCHARGE_HHEAR_U2_4HHEAR Urine Pool 2 (HHEAR_U2_50) 1
SA250661ReCHARGE_HHEAR_U2_2HHEAR Urine Pool 2 (HHEAR_U2_50) 1
SA250662ReCHARGE_HHEAR_U2_1HHEAR Urine Pool 2 (HHEAR_U2_50) 1
SA250663ReCHARGE_HHEAR_U2_8HHEAR Urine Pool 2 (HHEAR_U2_50) 2
SA250664ReCHARGE_HHEAR_U2_6HHEAR Urine Pool 2 (HHEAR_U2_50) 2
SA250665ReCHARGE_HHEAR_U2_5HHEAR Urine Pool 2 (HHEAR_U2_50) 2
SA250666ReCHARGE_HHEAR_U2_7HHEAR Urine Pool 2 (HHEAR_U2_50) 2
SA250667ReCHARGE_HHEAR_U2_11HHEAR Urine Pool 2 (HHEAR_U2_50) 3
SA250668ReCHARGE_HHEAR_U2_9HHEAR Urine Pool 2 (HHEAR_U2_50) 3
SA250669ReCHARGE_HHEAR_U2_10HHEAR Urine Pool 2 (HHEAR_U2_50) 3
SA250670ReCHARGE_NIST_3672_3NIST Urine Pool 3672 1
SA250671ReCHARGE_NIST_3672_2NIST Urine Pool 3672 1
SA250672ReCHARGE_NIST_3672_1NIST Urine Pool 3672 1
SA250673ReCHARGE_NIST_3672_6NIST Urine Pool 3672 2
SA250674ReCHARGE_NIST_3672_5NIST Urine Pool 3672 2
SA250675ReCHARGE_NIST_3672_4NIST Urine Pool 3672 2
SA250676ReCHARGE_NIST_3672_8NIST Urine Pool 3672 3
SA250677ReCHARGE_NIST_3672_7NIST Urine Pool 3672 3
SA250678ReCHARGE_SP_8Study Pool 1
SA250679ReCHARGE_SP_1Study Pool 1
SA250680ReCHARGE_SP_7Study Pool 1
SA250681ReCHARGE_SP_6Study Pool 1
SA250682ReCHARGE_SP_2Study Pool 1
SA250683ReCHARGE_SP_4Study Pool 1
SA250684ReCHARGE_SP_3Study Pool 1
SA250685ReCHARGE_SP_5Study Pool 1
SA250686ReCHARGE_SP_15Study Pool 2
SA250687ReCHARGE_SP_16Study Pool 2
SA250688ReCHARGE_SP_14Study Pool 2
SA250689ReCHARGE_SP_10Study Pool 2
SA250690ReCHARGE_SP_9Study Pool 2
SA250691ReCHARGE_SP_13Study Pool 2
SA250692ReCHARGE_SP_11Study Pool 2
SA250693ReCHARGE_SP_12Study Pool 2
SA250694ReCHARGE_SP_22Study Pool 3
SA250695ReCHARGE_SP_20Study Pool 3
SA250696ReCHARGE_SP_21Study Pool 3
SA250697ReCHARGE_SP_17Study Pool 3
SA250698ReCHARGE_SP_18Study Pool 3
SA250699ReCHARGE_SP_19Study Pool 3
SA250700ReCHARGE_S_54Study Sample 1
SA250701ReCHARGE_S_53Study Sample 1
SA250702ReCHARGE_S_52Study Sample 1
SA250703ReCHARGE_S_55Study Sample 1
SA250704ReCHARGE_S_56Study Sample 1
SA250705ReCHARGE_S_58Study Sample 1
SA250706ReCHARGE_S_57Study Sample 1
SA250707ReCHARGE_S_51Study Sample 1
SA250708ReCHARGE_S_59Study Sample 1
SA250709ReCHARGE_S_50Study Sample 1
SA250710ReCHARGE_S_45Study Sample 1
SA250711ReCHARGE_S_44Study Sample 1
SA250712ReCHARGE_S_43Study Sample 1
SA250713ReCHARGE_S_46Study Sample 1
SA250714ReCHARGE_S_47Study Sample 1
SA250715ReCHARGE_S_60Study Sample 1
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Collection:

Collection ID:CO002591
Collection Summary:NA
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002610
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP002604
Sampleprep Summary:Study samples (2 mL aliquots) were shipped from the University of California, Davis to the NC HHEAR Hub on dry ice. The NC HHEAR Hub thawed and transferred 50 µL of the study samples to a new set of tubes and used them for the analysis. An additional 10 µL was taken from the original study sample and transferred to another tube to make the total study pool for this project, and then distributed with 50 µL per aliquot, used as quality control study pools (QC study pools) throughout the whole analysis. All sample aliquots (50 µL each) and QC study pools (50 µL each) were stored at -80° C until the day of sample preparation. HHEAR Urine Pool 1 (50 µL each), HHEAR Urine Pool 2 (50 µL each), CHEAR reference urine (50 µL each) and NIST urine (SRM 3672) reference material (50 µL each) were provided by the NC HHEAR Hub. LC-MS grade water (50 µL) was used as blanks. All samples were thawed at 4°C overnight before the preparation. Samples, including study samples, study pool samples, HHEAR reference urine, CHEAR reference urine, NIST reference urine, and blanks were mixed with 400 µL methanol containing 500 ng/mL tryptophan-d5 as internal standard and vortexed by a multiple tube vortex mixer for 2 min at 5000 rpm at room temperature. All samples were centrifuged at 16,000 rcf for 10 min at 4°C. The supernatant (350 µL) was transferred into a pre-labeled 2.0 mL Lo-bind Eppendorf tube, dried by a SpeedVac overnight, and stored at -80° C. For immediate analysis, 100 µL of water-methanol solution (95:5, v/v) was used to reconstitute the dried extracts. Samples were thoroughly mixed on a multiple tube vortex mixer for 10 min at 5000 rpm at room temperature and then centrifuged at 4°C for 10 min at 16,000 rcf. The supernatant was transferred to pre-labeled autosampler vials for data acquisition by LC-MS.
Processing Storage Conditions:4℃
Extraction Method:Vortex with methanol containing 500ng/ml tryptophan-d5 as internal standard
Extract Storage:-80℃
Sample Resuspension:Water-Methanol (95:5, v/v)
Sample Spiking:Tryptophan-d5 stock solution at 500 ng/mL

Combined analysis:

Analysis ID AN004110
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap
Ion Mode POSITIVE
Units m/z

Chromatography:

Chromatography ID:CH003045
Chromatography Summary:Reverse phase
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Pressure:6000-10000
Column Temperature:50 oC
Flow Gradient:Time(min) Flow Rate %A %B Curve 1. 0 0.4 99.0 1.0 5 2. 1.00 0.4 99.0 1.0 5 3. 16.00 0.4 1.0 99.0 5 4. 19.00 0.4 1.0 99.0 5 5. 19.50 0.4 99.0 1.0 5 6. 22.00 0.4 99.0 1.0 5
Flow Rate:0.4 mL/min
Injection Temperature:8oC
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
Analytical Time:22 min
Chromatography Type:Reversed phase

MS:

MS ID:MS003857
Analysis ID:AN004110
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Instrument: Thermo Q Exactive HFx Software: Xcalibur 4.1.31.9 for data acquisition; Progenesis QI 2.4 for data preprocessing
Ion Mode:POSITIVE
Capillary Temperature:320 °C
Capillary Voltage:3.5 KV
Collision Energy:20-45, ramp
Collision Gas:N2
Dry Gas Flow:55
Dry Gas Temp:400°C
Fragment Voltage:ES+
Fragmentation Method:CID
Ion Spray Voltage:3.5kV
Ionization:ES+
Mass Accuracy:5 ppm
Dataformat:Profile
Desolvation Gas Flow:55
Desolvation Temperature:400 oC
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