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MB Sample ID: SA215823
Local Sample ID: | 9311 |
Subject ID: | SU002333 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002333 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
9311 | SA215823 | FL026049 | 24 months | host_age |
Collection:
Collection ID: | CO002326 |
Collection Summary: | Fecal samples were collected at birth (between 0 and 10 days post-delivery, median = 1 day, time point labeled as “birth”), during subsequent scheduled visits, and when possible during illness episodes. Stool samples were initially stored at -20°C at the International Centre for Diarrhoeal Disease Research (Bangladesh) and subsequently transferred to -80°C for shipment on dry ice to Nestlé Research where they were stored at -80°C until analysis. |
Sample Type: | Feces |
Treatment:
Treatment ID: | TR002345 |
Treatment Summary: | NA |
Sample Preparation:
Sampleprep ID: | SP002339 |
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 | AN003670 | AN003671 | AN003672 | AN003673 |
---|---|---|---|---|
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 | Abundances | Abundances | Unitless Abundances | Abundances |
Chromatography:
Chromatography ID: | CH002720 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Waters Atlantis HILIC (150 x 2mm,3um) |
Chromatography Type: | HILIC |
Chromatography ID: | CH002721 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH002722 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
Chromatography Type: | HILIC |
Chromatography ID: | CH002723 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Waters Acquity T3 (150 x 2.1 mm,1.7um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003421 |
Analysis ID: | AN003670 |
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: | MS003422 |
Analysis ID: | AN003671 |
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: | MS003423 |
Analysis ID: | AN003672 |
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: | MS003424 |
Analysis ID: | AN003673 |
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 |