Summary of Study ST002246

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 PR001434. The data can be accessed directly via it's Project DOI: 10.21228/M8C70Q 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.

Study ID	ST002246
Study Title	Longitudinal fecal metabolomic profiles from mothers and their infants in the EDIA study
Study Summary	In a cohort consisting of 32 mother-infant dyads, we profiled the fecal metabolome at birth and at 3 and 6 months of infant age. Metagenomes from the same samples were also generated.
Institute	Broad Institute of MIT and Harvard
Last Name	Xavier
First Name	Ramnik
Address	415 Main Street
Email	rxavier@broadinstitute.org
Phone	617717084
Submit Date	2022-08-02
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-11-23
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001434
Project DOI:	doi: 10.21228/M8C70Q
Project Title:	Longitudinal fecal metabolomic profiles from mothers and their infants in the EDIA study
Project Type:	Metabolomic profiling of human fecal samples
Project Summary:	In a cohort consisting of 32 mother-infant dyads, we profiled the fecal metabolome at birth and at 3 and 6 months of infant age. Metagenomes from the same samples were also generated.
Institute:	Broad Institute of MIT and Harvard
Last Name:	Xavier
First Name:	Ramnik
Address:	415 Main Street
Email:	rxavier@broadinstitute.org
Phone:	6177147080
Funding Source:	National Institutes of Health (P30 DK043351), Juvenile Diabetes Research Foundation (grant 2-SRA-2016-492 247-S-B)
Contributors:	Tommi Vatanen, Karolina S. Jabbar, Terhi Ruohtula, Jarno Honkanen, Julian Avila-Pacheco, Heli Siljander, Martin Stražar, Sami Oikarinen, Heikki Hyöty, Jorma Ilonen, Caroline M. Mitchell, Moran Yassour, Suvi M. Virtanen, Clary B. Clish, Damian R. Plichta, Hera Vlamakis, Mikael Knip, Ramnik J. Xavier

Subject:

Subject ID:	SU002332
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	mother.child
SA214630	301002	Child
SA214631	301005	Child
SA214632	301181	Child
SA214633	301003	Child
SA214634	301534	Child
SA214635	301837	Child
SA214636	301834	Child
SA214637	301051	Child
SA214638	301535	Child
SA214639	301253	Child
SA214640	301489	Child
SA214641	301271	Child
SA214642	301065	Child
SA214643	301492	Child
SA214644	301809	Child
SA214645	300299	Child
SA214646	301049	Child
SA214647	301490	Child
SA214648	301048	Child
SA214649	300200	Child
SA214650	301132	Child
SA214651	300473	Child
SA214652	300234	Child
SA214653	300474	Child
SA214654	300476	Child
SA214655	301101	Child
SA214656	301330	Child
SA214657	301099	Child
SA214658	300148	Child
SA214659	300147	Child
SA214660	300349	Child
SA214661	300202	Child
SA214662	300199	Child
SA214663	300505	Child
SA214664	300352	Child
SA214665	300151	Child
SA214666	300099	Child
SA214667	300379	Child
SA214668	300378	Child
SA214669	300171	Child
SA214670	300085	Child
SA214671	300081	Child
SA214672	301806	Child
SA214673	301568	Child
SA214674	301053	Child
SA214675	301565	Child
SA214676	301566	Child
SA214677	300082	Child
SA214678	301485	Child
SA214679	301275	Child
SA214680	301278	Child
SA214681	301776	Child
SA214682	301276	Child
SA214683	301487	Child
SA214684	301739	Child
SA214685	301484	Child
SA214686	301239	Child
SA214687	301056	Child
SA214688	301696	Child
SA214689	301698	Child
SA214690	301936	Child
SA214691	301695	Child
SA214692	300125	Child
SA214693	300122	Child
SA214694	300220	Child
SA214695	300123	Child
SA214696	301562	Child
SA214697	301264	Child
SA214698	301400	Child
SA214699	301403	Child
SA214700	301054	Child
SA214701	301401	Child
SA214702	301679	Child
SA214703	301262	Child
SA214704	301261	Child
SA214705	301098	Child
SA214706	300350	Child
SA214707	301126	Child
SA214708	300278	Child
SA214709	300279	Child
SA214710	301123	Child
SA214711	301124	Child
SA214712	301024	Child
SA214713	301613	Child
SA214714	300419	Child
SA214715	301865	Child
SA214716	301541	Child
SA214717	301545	Child
SA214718	301816	Child
SA214719	301540	Child
SA214720	302526	Child
SA214721	301864	Child
SA214722	301867	Child
SA214723	301021	Child
SA214724	301250	Child
SA214725	300382	Child
SA214726	300383	Child
SA214727	300386	Child
SA214728	301071	Child
SA214729	300096	Child

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Collection:

Collection ID:	CO002325
Collection Summary:	The participating women collected stool samples at home or in the delivery hospital. Infant stool samples were collected by the mothers at home and stored in the household freezer (−20°C) until the next visit to the study center. The samples were then shipped on dry ice to the EDIA Core Laboratory in Helsinki, where the samples were stored at −80°C.
Sample Type:	Feces

Treatment:

Treatment ID:	TR002344
Treatment Summary:	NA

Sample Preparation:

Sampleprep ID:	SP002338
Sampleprep Summary:	Stool samples were homogenized in 10 μL of water per milligram stool sample weight using a bead mill (TissueLyser II; Qiagen) and the aqueous homogenates were aliquoted for metabolite profiling analyses. LC-MS samples were prepared for four profiling methods as follows: HILIC-pos: Metabolites were extracted by adding 90 μL of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C8-pos: Lipids were extracted by adding 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, ambient temperature) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. HILIC-neg: Metabolites were extracted by adding 120 μL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C18-neg: Metabolites were extracted by adding 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis.

Sampleprep ID:

SP002338

Sampleprep Summary:

Stool samples were homogenized in 10 μL of water per milligram stool sample weight using a bead mill (TissueLyser II; Qiagen) and the aqueous homogenates were aliquoted for metabolite profiling analyses. LC-MS samples were prepared for four profiling methods as follows: HILIC-pos: Metabolites were extracted by adding 90 μL of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C8-pos: Lipids were extracted by adding 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, ambient temperature) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. HILIC-neg: Metabolites were extracted by adding 120 μL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C18-neg: Metabolites were extracted by adding 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis.

Combined analysis:

Analysis ID	AN003666	AN003667	AN003668	AN003669
Analysis type	MS	MS	MS	MS
Chromatography type	HILIC	Reversed phase	HILIC	Reversed phase
Chromatography system	Shimadzu Nexera X2	Shimadzu Nexera X2	Shimadzu Nexera X2	Shimadzu Nexera X2
Column	Waters Atlantis HILIC (150 x 2mm,3um)	Waters Acquity BEH C8 (100 x 2.1mm,1.7um)	Phenomenex Luna NH2 (150 x 2.1mm,3um)	Waters Acquity T3 (150 x 2.1 mm,1.7um)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	Orbitrap	Orbitrap	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	POSITIVE	NEGATIVE	NEGATIVE
Units	Unitless Abundances	Unitless Abundances	Unitless Abundances	Unitless Abundances

Chromatography:

Chromatography ID:	CH002716
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters Atlantis HILIC (150 x 2mm,3um)
Chromatography Type:	HILIC

Chromatography ID:	CH002717
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
Chromatography Type:	Reversed phase

Chromatography ID:	CH002718
Instrument Name:	Shimadzu Nexera X2
Column Name:	Phenomenex Luna NH2 (150 x 2.1mm,3um)
Chromatography Type:	HILIC

Chromatography ID:	CH002719
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters Acquity T3 (150 x 2.1 mm,1.7um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003417
Analysis ID:	AN003666
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.
Ion Mode:	POSITIVE

MS ID:	MS003418
Analysis ID:	AN003667
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.
Ion Mode:	POSITIVE

MS ID:	MS003419
Analysis ID:	AN003668
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.
Ion Mode:	NEGATIVE

MS ID:	MS003420
Analysis ID:	AN003669
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.
Ion Mode:	NEGATIVE