Summary of Study ST002757

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 PR001718. The data can be accessed directly via it's Project DOI: 10.21228/M8N41J 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 IDST002757
Study TitleThe ECHO Cohort Exposome: First Steps using HHEAR Analysis – An Opportunity for ALL ECHO Cohorts to Contribute Type A Samples – Untargeted Analysis (CIOB Cohort)
Study TypeProspective Cohort Study
Study SummaryCIOB is a prospective prenatal cohort study measuring maternal exposures to endocrine disrupting chemicals and place-based, perceptual, and biological markers of chronic psychosocial stressors and their relationships to adverse pregnancy outcomes and neurodevelopment in children. We have recruited nearly 800 pregnant participants from two locations in San Francisco; Zuckerberg San Francisco General Hospital (ZSFG), which serves primarily low income and Latinx patients, and Mission Bay Hospital (MB), which serves higher income and primarily white and Asian patients. We recruited women during their 2nd trimester (13 – 27 weeks) and collected biospecimens (urine, blood, hair, nails) and questionnaires during in-person visits, and umbilical cord and maternal blood and urine at delivery. We measured multiple classes of chemical exposures in our participants including flame retardants, per- and poly-fluoroalkyl substances (PFAS), phthalates, pesticides, phenols, aromatic amines, and we collaborated on development and implementation of shared standardized core data elements, questionnaires at multiple time points during pregnancy and childhood, and collection of biospecimens for chemical and mechanistic analyses during pregnancy and childhood. Please contact Erin DeMicco at erin.demicco@ucsf.edu for questions related to the subject characteristics and outcomes. 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. CIOB 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, San Francisco
DepartmentSchool of Medicine
Last NameWoodruff
First NameTracey
Address490 Illinois Street San Francisco CA 94158
EmailTracey.Woodruff@ucsf.edu
Phone(415) 476-3198
Submit Date2023-06-21
Total Subjects463
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 Date2024-06-24
Release Version1
Tracey Woodruff Tracey Woodruff
https://dx.doi.org/10.21228/M8N41J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001718
Project DOI:doi: 10.21228/M8N41J
Project Title:The ECHO Cohort Exposome: First Steps using HHEAR Analysis – An Opportunity for ALL ECHO Cohorts to Contribute Type A Samples – Untargeted Analysis (CIOB 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 , University of North Carolina at Chapel Hill, 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 CIOB 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:SU002864
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
SA289593CIOB_B_8Blank 1
SA289594CIOB_B_1Blank 1
SA289595CIOB_B_7Blank 1
SA289596CIOB_B_6Blank 1
SA289597CIOB_B_2Blank 1
SA289598CIOB_B_4Blank 1
SA289599CIOB_B_3Blank 1
SA289600CIOB_B_5Blank 1
SA289601CIOB_B_15Blank 2
SA289602CIOB_B_16Blank 2
SA289603CIOB_B_14Blank 2
SA289604CIOB_B_10Blank 2
SA289605CIOB_B_9Blank 2
SA289606CIOB_B_13Blank 2
SA289607CIOB_B_11Blank 2
SA289608CIOB_B_12Blank 2
SA289609CIOB_B_23Blank 3
SA289610CIOB_B_22Blank 3
SA289611CIOB_B_24Blank 3
SA289612CIOB_B_18Blank 3
SA289613CIOB_B_21Blank 3
SA289614CIOB_B_19Blank 3
SA289615CIOB_B_17Blank 3
SA289616CIOB_B_20Blank 3
SA289617CIOB_B_30Blank 4
SA289618CIOB_B_32Blank 4
SA289619CIOB_B_31Blank 4
SA289620CIOB_B_29Blank 4
SA289621CIOB_B_25Blank 4
SA289622CIOB_B_28Blank 4
SA289623CIOB_B_26Blank 4
SA289624CIOB_B_27Blank 4
SA289625CIOB_B_38Blank 5
SA289626CIOB_B_37Blank 5
SA289627CIOB_B_40Blank 5
SA289628CIOB_B_39Blank 5
SA289629CIOB_B_34Blank 5
SA289630CIOB_B_36Blank 5
SA289631CIOB_B_35Blank 5
SA289632CIOB_B_33Blank 5
SA289633CIOB_B_46Blank 6
SA289634CIOB_B_45Blank 6
SA289635CIOB_B_47Blank 6
SA289636CIOB_B_44Blank 6
SA289637CIOB_B_42Blank 6
SA289638CIOB_B_41Blank 6
SA289639CIOB_B_43Blank 6
SA289640CIOB_CHEAR_U_3CHEAR 1
SA289641CIOB_CHEAR_U_4CHEAR 1
SA289642CIOB_CHEAR_U_2CHEAR 1
SA289643CIOB_CHEAR_U_1CHEAR 1
SA289644CIOB_CHEAR_U_8CHEAR 2
SA289645CIOB_CHEAR_U_7CHEAR 2
SA289646CIOB_CHEAR_U_6CHEAR 2
SA289647CIOB_CHEAR_U_5CHEAR 2
SA289648CIOB_CHEAR_U_12CHEAR 3
SA289649CIOB_CHEAR_U_10CHEAR 3
SA289650CIOB_CHEAR_U_9CHEAR 3
SA289651CIOB_CHEAR_U_11CHEAR 3
SA289652CIOB_CHEAR_U_16CHEAR 4
SA289653CIOB_CHEAR_U_15CHEAR 4
SA289654CIOB_CHEAR_U_13CHEAR 4
SA289655CIOB_CHEAR_U_14CHEAR 4
SA289656CIOB_CHEAR_U_20CHEAR 5
SA289657CIOB_CHEAR_U_17CHEAR 5
SA289658CIOB_CHEAR_U_19CHEAR 5
SA289659CIOB_CHEAR_U_18CHEAR 5
SA289660CIOB_CHEAR_U_24CHEAR 6
SA289661CIOB_CHEAR_U_21CHEAR 6
SA289662CIOB_CHEAR_U_23CHEAR 6
SA289663CIOB_CHEAR_U_22CHEAR 6
SA289664CIOB_HHEAR_U1_4HHEAR U1 1
SA289665CIOB_HHEAR_U1_3HHEAR U1 1
SA289666CIOB_HHEAR_U1_2HHEAR U1 1
SA289667CIOB_HHEAR_U1_1HHEAR U1 1
SA289668CIOB_HHEAR_U1_8HHEAR U1 2
SA289669CIOB_HHEAR_U1_6HHEAR U1 2
SA289670CIOB_HHEAR_U1_5HHEAR U1 2
SA289671CIOB_HHEAR_U1_7HHEAR U1 2
SA289672CIOB_HHEAR_U1_12HHEAR U1 3
SA289673CIOB_HHEAR_U1_11HHEAR U1 3
SA289674CIOB_HHEAR_U1_9HHEAR U1 3
SA289675CIOB_HHEAR_U1_10HHEAR U1 3
SA289676CIOB_HHEAR_U1_16HHEAR U1 4
SA289677CIOB_HHEAR_U1_13HHEAR U1 4
SA289678CIOB_HHEAR_U1_15HHEAR U1 4
SA289679CIOB_HHEAR_U1_14HHEAR U1 4
SA289680CIOB_HHEAR_U1_20HHEAR U1 5
SA289681CIOB_HHEAR_U1_17HHEAR U1 5
SA289682CIOB_HHEAR_U1_19HHEAR U1 5
SA289683CIOB_HHEAR_U1_18HHEAR U1 5
SA289684CIOB_HHEAR_U1_24HHEAR U1 6
SA289685CIOB_HHEAR_U1_23HHEAR U1 6
SA289686CIOB_HHEAR_U1_22HHEAR U1 6
SA289687CIOB_HHEAR_U1_21HHEAR U1 6
SA289688CIOB_HHEAR_U2_4HHEAR U2 1
SA289689CIOB_HHEAR_U2_3HHEAR U2 1
SA289690CIOB_HHEAR_U2_2HHEAR U2 1
SA289691CIOB_HHEAR_U2_1HHEAR U2 1
SA289692CIOB_HHEAR_U2_8HHEAR U2 2
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Collection:

Collection ID:CO002857
Collection Summary:N/A
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002873
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP002870
Sampleprep Summary:Study samples were shipped from the UCSF School of Medicine 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 AN004474
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 Peak area

Chromatography:

Chromatography ID:CH003359
Chromatography Summary:Reversed phase
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Pressure:6000-10000 psi
Column Temperature:50 ℃
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:8 ℃
Internal Standard:Tryptophan-d5
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
Analytical Time:22 min
Weak Wash Solvent Name:10% methanol/90% water; 0.1% formic acid
Strong Wash Solvent Name:75% 2-Propanol/25% Water; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS004221
Analysis ID:AN004474
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
Fragmentation Method:CID
Ion Spray Voltage:3.5kV
Ionization:ES+
Mass Accuracy:5 ppm
Dataformat:Profile
Desolvation Gas Flow:55
Desolvation Temperature:400 ℃
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