Summary of Study ST001431

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	ST001431
Study Title	A Compromised Developmental Trajectory of the Infant Gut Microbiome and Metabolome in Atopic Eczema -(targeted SCFAs 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)	wiff
Analysis Type Detail	LC-MS
Release Date	2020-07-24
Release Version	1

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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:	SU001505
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
SA121486	SCFA_S96	Control
SA121487	SCFA_S97	Control
SA121488	SCFA_S95	Control
SA121489	SCFA_S1	Control
SA121490	SCFA_S93	Control
SA121491	SCFA_S103	Control
SA121492	SCFA_S104	Control
SA121493	SCFA_S114	Control
SA121494	SCFA_S113	Control
SA121495	SCFA_S106	Control
SA121496	SCFA_S105	Control
SA121497	SCFA_S92	Control
SA121498	SCFA_S85	Control
SA121499	SCFA_S66	Control
SA121500	SCFA_S67	Control
SA121501	SCFA_S65	Control
SA121502	SCFA_S61	Control
SA121503	SCFA_S60	Control
SA121504	SCFA_S72	Control
SA121505	SCFA_S73	Control
SA121506	SCFA_S115	Control
SA121507	SCFA_S82	Control
SA121508	SCFA_S81	Control
SA121509	SCFA_S80	Control
SA121510	SCFA_S86	Control
SA121511	SCFA_S116	Control
SA121512	SCFA_S170	Control
SA121513	SCFA_S171	Control
SA121514	SCFA_S169	Control
SA121515	SCFA_S149	Control
SA121516	SCFA_S148	Control
SA121517	SCFA_S172	Control
SA121518	SCFA_S175	Control
SA121519	SCFA_S184	Control
SA121520	SCFA_S183	Control
SA121521	SCFA_S177	Control
SA121522	SCFA_S176	Control
SA121523	SCFA_S147	Control
SA121524	SCFA_S144	Control
SA121525	SCFA_S125	Control
SA121526	SCFA_S123	Control
SA121527	SCFA_S122	Control
SA121528	SCFA_S121	Control
SA121529	SCFA_S126	Control
SA121530	SCFA_S127	Control
SA121531	SCFA_S143	Control
SA121532	SCFA_S142	Control
SA121533	SCFA_S132	Control
SA121534	SCFA_S131	Control
SA121535	SCFA_S59	Control
SA121536	SCFA_S94	Control
SA121537	SCFA_S11	Control
SA121538	SCFA_S14	Control
SA121539	SCFA_S42	Control
SA121540	SCFA_S10	Control
SA121541	SCFA_S9	Control
SA121542	SCFA_S23	Control
SA121543	SCFA_S8	Control
SA121544	SCFA_S41	Control
SA121545	SCFA_S40	Control
SA121546	SCFA_S31	Control
SA121547	SCFA_S32	Control
SA121548	SCFA_S30	Control
SA121549	SCFA_S29	Control
SA121550	SCFA_S39	Control
SA121551	SCFA_S38	Control
SA121552	SCFA_S22	Control
SA121553	SCFA_S43	Control
SA121554	SCFA_S50	Control
SA121555	SCFA_S21	Control
SA121556	SCFA_S3	Control
SA121557	SCFA_S51	Control
SA121558	SCFA_S52	Control
SA121559	SCFA_S57	Control
SA121560	SCFA_S56	Control
SA121561	SCFA_S53	Control
SA121562	SCFA_S49	Control
SA121563	SCFA_S2	Control
SA121564	SCFA_S15	Control
SA121565	SCFA_S48	Control
SA121566	SCFA_S16	Control
SA121567	SCFA_S17	Control
SA121568	SCFA_S145	Eczema
SA121569	SCFA_S154	Eczema
SA121570	SCFA_S153	Eczema
SA121571	SCFA_S151	Eczema
SA121572	SCFA_S152	Eczema
SA121573	SCFA_S150	Eczema
SA121574	SCFA_S140	Eczema
SA121575	SCFA_S146	Eczema
SA121576	SCFA_S141	Eczema
SA121577	SCFA_S13	Eczema
SA121578	SCFA_S12	Eczema
SA121579	SCFA_S155	Eczema
SA121580	SCFA_S166	Eczema
SA121581	SCFA_S7	Eczema
SA121582	SCFA_S174	Eczema
SA121583	SCFA_S173	Eczema
SA121584	SCFA_S168	Eczema
SA121585	SCFA_S6	Eczema

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Collection:

Collection ID:	CO001500
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:	TR001520
Treatment Summary:	Control vs Eczema (Non-allergen sensitized atopic eczema, Allergen-sensitiized atopic eczema)

Sample Preparation:

Sampleprep ID:	SP001513
Sampleprep Summary:	500 L of ice-cold extraction solvent (1:1 v/v ACN/water) containing 10 M of d5-benzoic acid as internal standard (IS) was added to 250 mg of wet stool sample and subjected to vortex mixing for 5 min at ambient temperature (24 ± 1 ◦C). The ratio of extraction solvent to wet sample weight was kept constant (2 L:1 mg) to prevent variable extraction efficiencies. The suspension was then centrifuged at 18 000g for 10 min at 4 ◦C. The supernatant was carefully removed and centrifuged again at 18 000g for 10 min at 4 ◦C. An aliquot of 100 L was subsequently derivatized using a final concentration of 10 mM aniline and 5 mM EDC for 2 h at 4 ◦C. The derivatization reaction was quenched using a final concentration of 18 mM succinic acid and 4.6 mM 2-mercaptoethanol for 2 h at 4 ◦C. An aliquot of each sample was further diluted 100-fold. All samples were stored at 4 ◦C until analysis on the same day

Sampleprep ID:

SP001513

Sampleprep Summary:

500 L of ice-cold extraction solvent (1:1 v/v ACN/water) containing 10 M of d5-benzoic acid as internal standard (IS) was added to 250 mg of wet stool sample and subjected to vortex mixing for 5 min at ambient temperature (24 ± 1 ◦C). The ratio of extraction solvent to wet sample weight was kept constant (2 L:1 mg) to prevent variable extraction efficiencies. The suspension was then centrifuged at 18 000g for 10 min at 4 ◦C. The supernatant was carefully removed and centrifuged again at 18 000g for 10 min at 4 ◦C. An aliquot of 100 L was subsequently derivatized using a final concentration of 10 mM aniline and 5 mM EDC for 2 h at 4 ◦C. The derivatization reaction was quenched using a final concentration of 18 mM succinic acid and 4.6 mM 2-mercaptoethanol for 2 h at 4 ◦C. An aliquot of each sample was further diluted 100-fold. All samples were stored at 4 ◦C until analysis on the same day

Combined analysis:

Analysis ID	AN002393
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Agilent 1290 Infinity
Column	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type	ESI
MS instrument type	Ion trap
MS instrument name	ABI Sciex 5500 QTrap
Ion Mode	POSITIVE
Units	nM

Chromatography:

Chromatography ID:	CH001759
Chromatography Summary:	Water and HPLC-grade isopropanol, both acidified with 0.1% formic acid were used as mobile phases A and B respectively. Chromatographic separation was achieved using an Acquity UPLC HSS T3 1.8 M, 2.1 mm x 100 mm column at a flow rate of 0.35 mL/min under the following condition: isocratic 15% B (0.00 − 2.00 min), linear gradient 15% to 33% B (2.01–6.00 min), linear gradient 33% to 34% B (6.01–7.50 min), linear gradient 34% to 36% B (7.51–12.00 min), isocratic 100% B (12.01–13.00 min), isocratic 15% B (13.01–15.00 min). Using an autosampler thermostatted at 4 ◦C, 1 L of each sample was injected onto the column maintained at 50 ◦C. The needle was flushed with methanol postinjection to minimize carry-over effect.
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Flow Gradient:	isocratic 15% B (0.00 - 2.00 min), linear gradient 15% to 33% B (2.01-6.00 min), linear gradient 33% to 34% B (6.01-7.50 min), linear gradient 34% to 36% B (7.51-12.00 min), isocratic 100% B (12.01-13.00 min), isocratic 15% B (13.01-15.00 min).
Flow Rate:	0.35 mL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% isopropanol; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002235
Analysis ID:	AN002393
Instrument Name:	ABI Sciex 5500 QTrap
Instrument Type:	Ion trap
MS Type:	ESI
MS Comments:	ion spray voltage, 5500 V; temperature, 500 ◦C; curtain gas, 20 psi; ion source gas 1, 18 psi; and ion source gas 2, 18 psi. Data were acquired in scheduled MRM mode using a 30 s detection window. More details available at Chan, J. C.; Kioh, D. Y.; Yap, G. C.; Lee, B. W.; Chan, E. C., A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with (12)C- and (13)C-labelled aniline. Journal of pharmaceutical and biomedical analysis 2017, 138, 43-53.
Ion Mode:	POSITIVE