Summary of Study ST001716

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 PR001100. The data can be accessed directly via it's Project DOI: 10.21228/M8HM61 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 IDST001716
Study TitleChemical co-exposures assessed via silicone wristbands and endogenous plasma metabolomics during pregnancy
Study TypeUntargeted Metabolomics Analysis
Study SummaryMetabolomics analysis was performed on maternal plasma samples obtained from the subjets in the New Hampshire Birth Cohort Study
Institute
University of North Carolina at Chapel Hill
DepartmentNutrition
LaboratoryMetabolomics and Exposome Laboratory at UNC Nutrition Research Institute
Last NameSumner
First NameSusan
Address500 Laureate Way, Kannapolis, NC, 28081, USA
EmailWimal_pathmasiri@unc.edu
Phone919-622-4456
Submit Date2021-03-03
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2022-03-04
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8HM61
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001100
Project DOI:doi: 10.21228/M8HM61
Project Title:Metabolomics in the New Hampshire Birth Cohort Study
Project Type:Metabolomics Analysis
Project Summary:Data were obtained from participants in the New Hampshire Birth Cohort Study, a prospective pregnancy cohort. Chemical co-exposures were assessed via silicone wristbands worn for one week at approximately 13 gestational weeks. Metabolomic features were assessed in maternal plasma samples obtained at ~24-28 gestational weeks via the Biocrates AbsoluteIDQ® p180 kit and nuclear magnetic resonance (NMR) spectroscopy. Associations between chemical co-exposures and plasma metabolomics were investigated using multivariate modeling to examine the association of chemical co-exposures on the maternal plasma metabolome during pregnancy.
Institute:Dartmouth College
Department:Department of Epidemiology
Last Name:Karagas
First Name:Margaret
Address:Geisel School of Medicine at Dartmouth, 1 Medical Center Drive, Williamson Translational Research Building, 7th Floor, Lebanon, NH 03756
Email:margaret.r.karagas@dartmouth.edu
Phone:919-541-6861
Funding Source:NIH, Office of the Director, UH3 OD023275, NIH NIEHS P42ES007373, and NIH NIGMS P20 GM104416. This project was supported by the Opportunities and Infrastructure Fund of the ECHO Program (EC0156; OIF PI: Romano, Cohort PI: Karagas
Project Comments:For further details, contact Margaret Karagass for information on the New Hampshire Birth Cohort Study

Subject:

Subject ID:SU001793
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 phenotype nmr_batch
SA161662S_869Maternal Batch 10
SA161663S_868Maternal Batch 10
SA161664S_866Maternal Batch 10
SA161665S_870Maternal Batch 10
SA161666S_867Maternal Batch 10
SA161667S_872Maternal Batch 10
SA161668S_875Maternal Batch 10
SA161669S_874Maternal Batch 10
SA161670S_873Maternal Batch 10
SA161671S_865Maternal Batch 10
SA161672S_871Maternal Batch 10
SA161673S_864Maternal Batch 10
SA161674S_857Maternal Batch 10
SA161675S_856Maternal Batch 10
SA161676S_854Maternal Batch 10
SA161677S_853Maternal Batch 10
SA161678S_858Maternal Batch 10
SA161679S_859Maternal Batch 10
SA161680S_862Maternal Batch 10
SA161681S_861Maternal Batch 10
SA161682S_860Maternal Batch 10
SA161683S_880Maternal Batch 10
SA161684S_885Maternal Batch 10
SA161685S_907Maternal Batch 10
SA161686S_906Maternal Batch 10
SA161687S_902Maternal Batch 10
SA161688S_901Maternal Batch 10
SA161689S_909Maternal Batch 10
SA161690S_910Maternal Batch 10
SA161691S_916Maternal Batch 10
SA161692S_915Maternal Batch 10
SA161693S_913Maternal Batch 10
SA161694S_912Maternal Batch 10
SA161695S_898Maternal Batch 10
SA161696S_897Maternal Batch 10
SA161697S_888Maternal Batch 10
SA161698S_887Maternal Batch 10
SA161699S_886Maternal Batch 10
SA161700S_852Maternal Batch 10
SA161701S_889Maternal Batch 10
SA161702S_891Maternal Batch 10
SA161703S_895Maternal Batch 10
SA161704S_894Maternal Batch 10
SA161705S_892Maternal Batch 10
SA161706S_883Maternal Batch 10
SA161707S_851Maternal Batch 10
SA161708S_827Maternal Batch 10
SA161709S_823Maternal Batch 10
SA161710S_828Maternal Batch 10
SA161711S_829Maternal Batch 10
SA161712S_831Maternal Batch 10
SA161713S_821Maternal Batch 10
SA161714S_820Maternal Batch 10
SA161715S_921Maternal Batch 10
SA161716S_920Maternal Batch 10
SA161717S_917Maternal Batch 10
SA161718S_918Maternal Batch 10
SA161719S_832Maternal Batch 10
SA161720S_919Maternal Batch 10
SA161721S_846Maternal Batch 10
SA161722S_847Maternal Batch 10
SA161723S_848Maternal Batch 10
SA161724S_834Maternal Batch 10
SA161725S_845Maternal Batch 10
SA161726S_850Maternal Batch 10
SA161727S_838Maternal Batch 10
SA161728S_839Maternal Batch 10
SA161729S_841Maternal Batch 10
SA161730S_844Maternal Batch 10
SA161731S_843Maternal Batch 10
SA161732S_893Maternal Batch 11
SA161733S_877Maternal Batch 11
SA161734S_899Maternal Batch 11
SA161735S_879Maternal Batch 11
SA161736S_881Maternal Batch 11
SA161737S_903Maternal Batch 11
SA161738S_876Maternal Batch 11
SA161739S_922Maternal Batch 11
SA161740S_904Maternal Batch 11
SA161741S_900Maternal Batch 11
SA161742S_833Maternal Batch 11
SA161743S_826Maternal Batch 11
SA161744S_825Maternal Batch 11
SA161745S_819Maternal Batch 11
SA161746S_830Maternal Batch 11
SA161747S_836Maternal Batch 11
SA161748S_855Maternal Batch 11
SA161749S_849Maternal Batch 11
SA161750S_840Maternal Batch 11
SA161751S_863Maternal Batch 11
SA161752S_835Maternal Batch 11
SA161753S_1358Maternal Batch 16
SA161754S_1357Maternal Batch 16
SA161755S_1356Maternal Batch 16
SA161756S_1359Maternal Batch 16
SA161757S_1361Maternal Batch 16
SA161758S_1367Maternal Batch 16
SA161759S_1366Maternal Batch 16
SA161760S_1363Maternal Batch 16
SA161761S_1354Maternal Batch 16
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Collection:

Collection ID:CO001786
Collection Summary:At the mother’s clinical prenatal blood draw at 24-28 gestational weeks (mean=28 week; range 20-38 weeks), the New Hampshire Birth Cohort Study requests and processes a small sample of blood, using a 6 ml potassium K2 EDTA 10.8 mg royal blue top tube. Plasma samples are stored at -80C.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001806
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP001799
Sampleprep Summary:Aliquots of each de-identified sample were received by the NIH ERCMRC on dry ice and immediately stored at -80 °C after being logged in for metabolomics analysis. The samples were randomized into NMR batches for processing and data acquisition. Samples of each NMR batch was prepared as follows. The study plasma samples were thawed at 4°C overnight. An aliquot (350 µL) of thawed plasma was transferred into labeled 2.0 mL LoBind Eppendorf tubes. Low volume samples that were below 350 µL were made up to 350 µL with water. A volume of 1050 µL of Methanol was added to each sample, vortexed for 2 min on multi-tube vortexer at speed 5, centrifuged at 16,000 rcf for 20 min. A 1000 µL aliquot of clean supernatant was transferred into new pre-labeled LoBind Eppendorf tubes, dried on the SpeedVac. The dried extracts of samples were reconstituted in 700 µL of D2O Phosphate buffer NMR Master Mix (containing 0.5 mM DSS-d6 and 0.2% NaN3 (w/v) in D2O). The sample was vortexed for 2 min on multi-tube vortexer at speed 5, centrifuged at 12,000 rcf for 4 min., and a 600 µL aliquot of the supernatant was transferred into numbered 5 mm NMR tubes. Aliquots (350 of µL) CHEAR Plasma Reference (QC) samples were included in each NMR batch, processed exactly similar to the study samples described above, and used for QC purposes.
Sampleprep Protocol Filename:Dartmouth-ECHO Plasma Metabolomics Procedures

Analysis:

Analysis ID:AN002796
Laboratory Name:Metabolomics and Exposome Lab at UNC Nutrition Research Institute
Analysis Type:NMR
Software Version:TopSpin 3.5
Operator Name:Wimal Pathmasiri, Kevin Knagge
Detector Type:NMR
Data Format:fid, 1r

NMR:

NMR ID:NM000203
Analysis ID:AN002796
Instrument Name:Avance III 700 MHz NMR Spectrometer
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Field Frequency Lock:3015 Hz, D2O
Standard Concentration:0.5 mM
Spectrometer Frequency:700 MHz
NMR Probe:CP QCI/HPCN
NMR Solvent:90% H2O, 10% D2O
NMR Tube Size:5 mm
Shimming Method:topshim
Pulse Sequence:noesygppr1d
Water Suppression:pre-saturation
Pulse Width:15.57 us
Power Level:12.3 Watts
Receiver Gain:32
Offset Frequency:3289.21
Presaturation Power Level:0.0000964 Watts
Chemical Shift Ref Cpd:DSS-d6
Temperature:25 C
Number Of Scans:128
Dummy Scans:4
Acquisition Time:3.9 seconds
Relaxation Delay:2 seconds
Spectral Width:12 ppm
Num Data Points Acquired:65536
Real Data Points:32768
Line Broadening:0.5 Hz
Zero Filling:Yes
Apodization:Lorentzian
Baseline Correction Method:Polynomial
Chemical Shift Ref Std:DSS-d6
Binned Increment:0.04ppm
Binned Data Excluded Range:2.53 - 2.62 ppm (EDTA 01), 2.68 - 2.72 ppm (EDTA 02 ), 3.03 - 3.37 ppm (Methanol), 3.57 - 3.66 ppm (EDTA 03 ), 4.79-4.90 ppm (Water)
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