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

Study ID	ST001432
Study Title	A Compromised Developmental Trajectory of the Infant Gut Microbiome and Metabolome in Atopic Eczema - (untargeted global metabolomics profiling) )
Study 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
Submit Date	2020-05-28
Num Groups	3
Total Subjects	63
Raw Data Available	Yes
Raw Data File Type(s)	peg
Analysis Type Detail	GC-MS
Release Date	2020-07-24
Release Version	1

Select appropriate tab below to view additional metadata details:

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
SA121648	Global_S96	Control
SA121649	Global_S97	Control
SA121650	Global_S95	Control
SA121651	Global_S1	Control
SA121652	Global_S93	Control
SA121653	Global_S103	Control
SA121654	Global_S104	Control
SA121655	Global_S114	Control
SA121656	Global_S113	Control
SA121657	Global_S106	Control
SA121658	Global_S105	Control
SA121659	Global_S92	Control
SA121660	Global_S85	Control
SA121661	Global_S66	Control
SA121662	Global_S67	Control
SA121663	Global_S65	Control
SA121664	Global_S61	Control
SA121665	Global_S60	Control
SA121666	Global_S72	Control
SA121667	Global_S73	Control
SA121668	Global_S115	Control
SA121669	Global_S82	Control
SA121670	Global_S81	Control
SA121671	Global_S80	Control
SA121672	Global_S86	Control
SA121673	Global_S116	Control
SA121674	Global_S170	Control
SA121675	Global_S171	Control
SA121676	Global_S169	Control
SA121677	Global_S149	Control
SA121678	Global_S148	Control
SA121679	Global_S172	Control
SA121680	Global_S175	Control
SA121681	Global_S184	Control
SA121682	Global_S183	Control
SA121683	Global_S177	Control
SA121684	Global_S176	Control
SA121685	Global_S147	Control
SA121686	Global_S144	Control
SA121687	Global_S125	Control
SA121688	Global_S123	Control
SA121689	Global_S122	Control
SA121690	Global_S121	Control
SA121691	Global_S126	Control
SA121692	Global_S127	Control
SA121693	Global_S143	Control
SA121694	Global_S142	Control
SA121695	Global_S132	Control
SA121696	Global_S131	Control
SA121697	Global_S59	Control
SA121698	Global_S94	Control
SA121699	Global_S11	Control
SA121700	Global_S14	Control
SA121701	Global_S42	Control
SA121702	Global_S10	Control
SA121703	Global_S9	Control
SA121704	Global_S23	Control
SA121705	Global_S8	Control
SA121706	Global_S41	Control
SA121707	Global_S40	Control
SA121708	Global_S31	Control
SA121709	Global_S32	Control
SA121710	Global_S30	Control
SA121711	Global_S29	Control
SA121712	Global_S39	Control
SA121713	Global_S38	Control
SA121714	Global_S22	Control
SA121715	Global_S43	Control
SA121716	Global_S50	Control
SA121717	Global_S21	Control
SA121718	Global_S3	Control
SA121719	Global_S51	Control
SA121720	Global_S52	Control
SA121721	Global_S57	Control
SA121722	Global_S56	Control
SA121723	Global_S53	Control
SA121724	Global_S49	Control
SA121725	Global_S2	Control
SA121726	Global_S15	Control
SA121727	Global_S48	Control
SA121728	Global_S16	Control
SA121729	Global_S17	Control
SA121730	Global_S145	Eczema
SA121731	Global_S154	Eczema
SA121732	Global_S153	Eczema
SA121733	Global_S151	Eczema
SA121734	Global_S152	Eczema
SA121735	Global_S150	Eczema
SA121736	Global_S140	Eczema
SA121737	Global_S146	Eczema
SA121738	Global_S141	Eczema
SA121739	Global_S13	Eczema
SA121740	Global_S12	Eczema
SA121741	Global_S155	Eczema
SA121742	Global_S166	Eczema
SA121743	Global_S7	Eczema
SA121744	Global_S174	Eczema
SA121745	Global_S173	Eczema
SA121746	Global_S168	Eczema
SA121747	Global_S6	Eczema

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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.

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