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.

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Study IDST002246
Study TitleLongitudinal fecal metabolomic profiles from mothers and their infants in the EDIA study
Study SummaryIn 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 NameXavier
First NameRamnik
Address415 Main Street
Emailrxavier@broadinstitute.org
Phone617717084
Submit Date2022-08-02
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-11-23
Release Version1
Ramnik Xavier Ramnik Xavier
https://dx.doi.org/10.21228/M8C70Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA214630301002Child
SA214631301005Child
SA214632301181Child
SA214633301003Child
SA214634301534Child
SA214635301837Child
SA214636301834Child
SA214637301051Child
SA214638301535Child
SA214639301253Child
SA214640301489Child
SA214641301271Child
SA214642301065Child
SA214643301492Child
SA214644301809Child
SA214645300299Child
SA214646301049Child
SA214647301490Child
SA214648301048Child
SA214649300200Child
SA214650301132Child
SA214651300473Child
SA214652300234Child
SA214653300474Child
SA214654300476Child
SA214655301101Child
SA214656301330Child
SA214657301099Child
SA214658300148Child
SA214659300147Child
SA214660300349Child
SA214661300202Child
SA214662300199Child
SA214663300505Child
SA214664300352Child
SA214665300151Child
SA214666300099Child
SA214667300379Child
SA214668300378Child
SA214669300171Child
SA214670300085Child
SA214671300081Child
SA214672301806Child
SA214673301568Child
SA214674301053Child
SA214675301565Child
SA214676301566Child
SA214677300082Child
SA214678301485Child
SA214679301275Child
SA214680301278Child
SA214681301776Child
SA214682301276Child
SA214683301487Child
SA214684301739Child
SA214685301484Child
SA214686301239Child
SA214687301056Child
SA214688301696Child
SA214689301698Child
SA214690301936Child
SA214691301695Child
SA214692300125Child
SA214693300122Child
SA214694300220Child
SA214695300123Child
SA214696301562Child
SA214697301264Child
SA214698301400Child
SA214699301403Child
SA214700301054Child
SA214701301401Child
SA214702301679Child
SA214703301262Child
SA214704301261Child
SA214705301098Child
SA214706300350Child
SA214707301126Child
SA214708300278Child
SA214709300279Child
SA214710301123Child
SA214711301124Child
SA214712301024Child
SA214713301613Child
SA214714300419Child
SA214715301865Child
SA214716301541Child
SA214717301545Child
SA214718301816Child
SA214719301540Child
SA214720302526Child
SA214721301864Child
SA214722301867Child
SA214723301021Child
SA214724301250Child
SA214725300382Child
SA214726300383Child
SA214727300386Child
SA214728301071Child
SA214729300096Child
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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.

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 2 mm, 3 μm) 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, 1.7 um)
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 2 mm, 3 μm)
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, 1.7 um)
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
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