Summary of Study ST002780

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 PR001735. The data can be accessed directly via it's Project DOI: 10.21228/M8FD83 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 IDST002780
Study TitleThe ECHO Cohort Exposome: First Steps using HHEAR Analysis – An Opportunity for ALL ECHO Cohorts to Contribute Type A Samples – Untargeted Analysis (CANDLE Cohort)
Study TypeProspective Cohort Study
Study SummaryThe CANDLE study is a contemporary birth cohort representing a racially and socioeconomically diverse southern metropolitan population of the US. It was designed to investigate the effects of different factors, such as prenatal characteristics, home environment, childhood experiences, genetics, and exposure to potentially harmful substances on the neurocognitive development of children from birth to age four years. The CANDLE study enrolled a total of 1,503 healthy women during their 2nd trimester of pregnancy at four hospitals in Memphis, TN. The sample accrued between 2006 and 2011, demographically representing Shelby County TN, a highly disadvantaged urban population. Study participants are primarily African American and White. 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. CANDLE 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 Tennessee Health Science Center
DepartmentPreventive Medicine
Last NameZhao
First NameQi
Address633 Doctors Office Building Memphis, TN 38163
Emailqzhao11@uthsc.edu
Phone(901) 448 2732
Submit Date2023-07-11
Total Subjects758
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 Date2024-07-15
Release Version1
Qi Zhao Qi Zhao
https://dx.doi.org/10.21228/M8FD83
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001735
Project DOI:doi: 10.21228/M8FD83
Project Title:The ECHO Cohort Exposome: First Steps using HHEAR Analysis – An Opportunity for ALL ECHO Cohorts to Contribute Type A Samples – Untargeted Analysis (CANDLE 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 CANDLE 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:SU002887
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
SA298520CANDLE_B_7blank 1
SA298521CANDLE_B_6blank 1
SA298522CANDLE_B_5blank 1
SA298523CANDLE_B_8blank 1
SA298524CANDLE_B_2blank 1
SA298525CANDLE_B_1blank 1
SA298526CANDLE_B_4blank 1
SA298527CANDLE_B_3blank 1
SA298528CANDLE_B_73blank 10
SA298529CANDLE_B_74blank 10
SA298530CANDLE_B_76blank 10
SA298531CANDLE_B_75blank 10
SA298532CANDLE_B_14blank 2
SA298533CANDLE_B_15blank 2
SA298534CANDLE_B_13blank 2
SA298535CANDLE_B_16blank 2
SA298536CANDLE_B_9blank 2
SA298537CANDLE_B_12blank 2
SA298538CANDLE_B_11blank 2
SA298539CANDLE_B_10blank 2
SA298540CANDLE_B_23blank 3
SA298541CANDLE_B_24blank 3
SA298542CANDLE_B_17blank 3
SA298543CANDLE_B_22blank 3
SA298544CANDLE_B_21blank 3
SA298545CANDLE_B_19blank 3
SA298546CANDLE_B_18blank 3
SA298547CANDLE_B_20blank 3
SA298548CANDLE_B_30blank 4
SA298549CANDLE_B_31blank 4
SA298550CANDLE_B_32blank 4
SA298551CANDLE_B_29blank 4
SA298552CANDLE_B_25blank 4
SA298553CANDLE_B_28blank 4
SA298554CANDLE_B_26blank 4
SA298555CANDLE_B_27blank 4
SA298556CANDLE_B_35blank 5
SA298557CANDLE_B_36blank 5
SA298558CANDLE_B_33blank 5
SA298559CANDLE_B_34blank 5
SA298560CANDLE_B_39blank 5
SA298561CANDLE_B_37blank 5
SA298562CANDLE_B_40blank 5
SA298563CANDLE_B_38blank 5
SA298564CANDLE_B_46blank 6
SA298565CANDLE_B_48blank 6
SA298566CANDLE_B_45blank 6
SA298567CANDLE_B_47blank 6
SA298568CANDLE_B_44blank 6
SA298569CANDLE_B_42blank 6
SA298570CANDLE_B_41blank 6
SA298571CANDLE_B_43blank 6
SA298572CANDLE_B_54blank 7
SA298573CANDLE_B_55blank 7
SA298574CANDLE_B_53blank 7
SA298575CANDLE_B_56blank 7
SA298576CANDLE_B_50blank 7
SA298577CANDLE_B_49blank 7
SA298578CANDLE_B_51blank 7
SA298579CANDLE_B_52blank 7
SA298580CANDLE_B_63blank 8
SA298581CANDLE_B_58blank 8
SA298582CANDLE_B_57blank 8
SA298583CANDLE_B_59blank 8
SA298584CANDLE_B_60blank 8
SA298585CANDLE_B_62blank 8
SA298586CANDLE_B_61blank 8
SA298587CANDLE_B_64blank 8
SA298588CANDLE_B_67blank 9
SA298589CANDLE_B_66blank 9
SA298590CANDLE_B_65blank 9
SA298591CANDLE_B_68blank 9
SA298592CANDLE_B_69blank 9
SA298593CANDLE_B_71blank 9
SA298594CANDLE_B_70blank 9
SA298595CANDLE_B_72blank 9
SA297543CANDLE_CHEAR_U_4CHEAR 1
SA297544CANDLE_CHEAR_U_1CHEAR 1
SA297545CANDLE_CHEAR_U_2CHEAR 1
SA297546CANDLE_CHEAR_U_3CHEAR 1
SA297547CANDLE_CHEAR_U_37CHEAR 10
SA297548CANDLE_CHEAR_U_38CHEAR 10
SA297549CANDLE_CHEAR_U_5CHEAR 2
SA297550CANDLE_CHEAR_U_6CHEAR 2
SA297551CANDLE_CHEAR_U_8CHEAR 2
SA297552CANDLE_CHEAR_U_7CHEAR 2
SA297553CANDLE_CHEAR_U_9CHEAR 3
SA297554CANDLE_CHEAR_U_12CHEAR 3
SA297555CANDLE_CHEAR_U_11CHEAR 3
SA297556CANDLE_CHEAR_U_10CHEAR 3
SA297557CANDLE_CHEAR_U_13CHEAR 4
SA297558CANDLE_CHEAR_U_15CHEAR 4
SA297559CANDLE_CHEAR_U_14CHEAR 4
SA297560CANDLE_CHEAR_U_16CHEAR 4
SA297561CANDLE_CHEAR_U_18CHEAR 5
SA297562CANDLE_CHEAR_U_20CHEAR 5
SA297563CANDLE_CHEAR_U_19CHEAR 5
SA297564CANDLE_CHEAR_U_17CHEAR 5
SA297565CANDLE_CHEAR_U_23CHEAR 6
SA297566CANDLE_CHEAR_U_24CHEAR 6
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Collection:

Collection ID:CO002880
Collection Summary:N/A
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002896
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP002893
Sampleprep Summary:Study samples were shipped from the University of Tennessee Health Science Center 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 AN004527
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 Normalized intensity

Chromatography:

Chromatography ID:CH003400
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:MS004274
Analysis ID:AN004527
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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