Summary of Study ST001432

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 PR000983. The data can be accessed directly via it's Project DOI: 10.21228/M8N104 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST001432
Study TitleA Compromised Developmental Trajectory of the Infant Gut Microbiome and Metabolome in Atopic Eczema - (untargeted global metabolomics profiling) )
Study SummaryEvidence is accumulating that the establishment of the gut microbiome in early life influences the development of atopic eczema. In this longitudinal study, we used integrated multi-omics analyses to infer functional mechanisms by which the microbiome modulates atopic eczema risk.
Institute
National University of Singapore
Last NameTa
First NameLe Duc Huy
AddressMD1 - Tahir Foundation Building (MD1), Level 15, Department of Paediatrics, Allergy & Immunology Division, National University of Singapore (NUS), 12 Science Drive 2. Singapore 117549
Emailhuy.taleduc13@sps.nus.edu.sg
Phone6596123681
Submit Date2020-05-28
Num Groups3
Total Subjects63
Raw Data AvailableYes
Raw Data File Type(s)peg
Analysis Type DetailGC-MS
Release Date2020-07-24
Release Version1
Le Duc Huy Ta Le Duc Huy Ta
https://dx.doi.org/10.21228/M8N104
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000983
Project DOI:doi: 10.21228/M8N104
Project Title:A Compromised Developmental Trajectory of the Infant Gut Microbiome and Metabolome in Atopic Eczema
Project Summary:Evidence is accumulating that the establishment of the gut microbiome in early life influences the development of atopic eczema. In this longitudinal study, we used integrated multi-omics analyses to infer functional mechanisms by which the microbiome modulates atopic eczema risk.
Institute:National University of Singapore
Last Name:Ta
First Name:Le Duc Huy
Address:MD1 - Tahir Foundation Building (MD1), Level 15, Department of Paediatrics, Allergy & Immunology Division, National University of Singapore (NUS), 12 Science Drive 2. Singapore 117549
Email:huy.taleduc13@sps.nus.edu.sg
Phone:6596123681

Subject:

Subject ID:SU001506
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 Treatment
SA121648Global_S96Control
SA121649Global_S97Control
SA121650Global_S95Control
SA121651Global_S1Control
SA121652Global_S93Control
SA121653Global_S103Control
SA121654Global_S104Control
SA121655Global_S114Control
SA121656Global_S113Control
SA121657Global_S106Control
SA121658Global_S105Control
SA121659Global_S92Control
SA121660Global_S85Control
SA121661Global_S66Control
SA121662Global_S67Control
SA121663Global_S65Control
SA121664Global_S61Control
SA121665Global_S60Control
SA121666Global_S72Control
SA121667Global_S73Control
SA121668Global_S115Control
SA121669Global_S82Control
SA121670Global_S81Control
SA121671Global_S80Control
SA121672Global_S86Control
SA121673Global_S116Control
SA121674Global_S170Control
SA121675Global_S171Control
SA121676Global_S169Control
SA121677Global_S149Control
SA121678Global_S148Control
SA121679Global_S172Control
SA121680Global_S175Control
SA121681Global_S184Control
SA121682Global_S183Control
SA121683Global_S177Control
SA121684Global_S176Control
SA121685Global_S147Control
SA121686Global_S144Control
SA121687Global_S125Control
SA121688Global_S123Control
SA121689Global_S122Control
SA121690Global_S121Control
SA121691Global_S126Control
SA121692Global_S127Control
SA121693Global_S143Control
SA121694Global_S142Control
SA121695Global_S132Control
SA121696Global_S131Control
SA121697Global_S59Control
SA121698Global_S94Control
SA121699Global_S11Control
SA121700Global_S14Control
SA121701Global_S42Control
SA121702Global_S10Control
SA121703Global_S9Control
SA121704Global_S23Control
SA121705Global_S8Control
SA121706Global_S41Control
SA121707Global_S40Control
SA121708Global_S31Control
SA121709Global_S32Control
SA121710Global_S30Control
SA121711Global_S29Control
SA121712Global_S39Control
SA121713Global_S38Control
SA121714Global_S22Control
SA121715Global_S43Control
SA121716Global_S50Control
SA121717Global_S21Control
SA121718Global_S3Control
SA121719Global_S51Control
SA121720Global_S52Control
SA121721Global_S57Control
SA121722Global_S56Control
SA121723Global_S53Control
SA121724Global_S49Control
SA121725Global_S2Control
SA121726Global_S15Control
SA121727Global_S48Control
SA121728Global_S16Control
SA121729Global_S17Control
SA121730Global_S145Eczema
SA121731Global_S154Eczema
SA121732Global_S153Eczema
SA121733Global_S151Eczema
SA121734Global_S152Eczema
SA121735Global_S150Eczema
SA121736Global_S140Eczema
SA121737Global_S146Eczema
SA121738Global_S141Eczema
SA121739Global_S13Eczema
SA121740Global_S12Eczema
SA121741Global_S155Eczema
SA121742Global_S166Eczema
SA121743Global_S7Eczema
SA121744Global_S174Eczema
SA121745Global_S173Eczema
SA121746Global_S168Eczema
SA121747Global_S6Eczema
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Collection:

Collection ID:CO001501
Collection Summary:Stool samples were collected by the parents using sterile faeces containers and stored at -20oC at home. Samples were then transported to the lab in cold chain within 20 hours of sample collection for processing. After processing, sample were stored at -80oC until further analysis.
Sample Type:Feces
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001521
Treatment Summary:Control vs Eczema (Non-allergen sensitized atopic eczema, Allergen-sensitiized atopic eczema)

Sample Preparation:

Sampleprep ID:SP001514
Sampleprep Summary:For global profiling of stool metabolites, samples were randomized then processed according to our in-house protocol. Briefly, lyophilized stool sample (80 mg) was ultrasonicated with 1 mL of ice-cold extraction solvent (methanol:water [8:2]) containing 1 µg/mL d27-myristic acid as an internal standard at 4°C in a bath ultrasonicator (Elma Transsonic 460, Germany) for 30 min, and vortex-mixed for 2 min. The samples were then centrifuged at 18,000 g for 20 min at 4°C, and 0.5 mL of the supernatant was extracted carefully followed by drying at 50°C under a gentle stream of nitrogen gas (Turbovap LV, Caliper Life Sciences, Hopkinton, MA, USA). 100 µL of toluene (kept anhydrous with sodium sulfate) was added to the dry residue and evaporated completely again at 50°C under nitrogen gas to remove traces of water. The dried metabolic extract was then oximated with 50 µL of MOX (20 mg/mL) at 60°C for 2 h. Following centrifugation, 100 µL of MSTFA with 1% TMCS was added and the mixture was incubated at 60°C for 45 min to form trimethylsilyl (TMS) derivatives. Finally, 100 µL of the TMS derivatives was transferred into a GC vial and subjected to gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) analysis. 50 µL of each stool extract prepared during extraction of lyophilized stool were also pooled to prepare quality control (QC) samples.

Combined analysis:

Analysis ID AN002394
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column Agilent DB-1 DB-1 (30 m × 250 um i.d.)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units Ion Count Per Second

Chromatography:

Chromatography ID:CH001760
Chromatography Summary:Helium was employed as the carrier gas at a constant flow rate of 1.5 mL/min and the injector split ratio was adjusted to 1:10. An injection volume of 1 µL was used. The injector, transfer line and ionsource temperatures were maintained at 220, 280 and 250°C, respectively. The oven temperature was programmed at 70°C for 0.2 min, increased at 9°C/min to 270°C where it was sustained for 5 min, and further increased at 40°C/min to 310°C where it was held for 11 min. The mass spectrometer was operated in the electron impact ionization mode at 70 eV. Data were acquired in full scan mode from m/z 40 to 600 with an acquisition rate of 20 spectra per second. To detect retention time shifts and facilitate Kovats retention index (RI) calculation, a standard alkane series mixture (C7-C30) was injected before every batch during sample analysis. This was accompanied by an injection of one pooled QC after every injection of 10 samples.
Instrument Name:Agilent 7890A
Column Name:Agilent DB-1 DB-1 (30 m × 250 um i.d.)
Chromatography Type:GC

MS:

MS ID:MS002236
Analysis ID:AN002394
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:The mass spectrometer was operated in the electron impact ionization mode at 70 eV. Data were acquired in full scan mode from m/z 40 to 600 with an acquisition rate of 20 spectra per second.
Ion Mode:POSITIVE
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