Summary of study ST000343

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 PR000275. The data can be accessed directly via it's Project DOI: 10.21228/M87K5T This work is supported by NIH grant, U2C- DK119886.

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Study IDST000343
Study TitleModification of metabolites by gut microbiota in response to diet
Study SummaryThis experiment is looking at effects of diets on rats. Specifically how those diets might alter metabolites that could be modified by gut microbiota and in particular indoles and bile salts.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2016-02-05
Num Groups4
Total Subjects68
Raw Data AvailableYes
Raw Data File Type(s).bin,.cg,.cd,.xml
Analysis Type DetailLC-MS
Release Date2016-03-03
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M87K5T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000275
Project DOI:doi: 10.21228/M87K5T
Project Title:Modification of metabolites by gut microbiota in response to diet
Project Summary:This experiment is looking at effects of diets on rats. Specifically how those diets might alter metabolites that could be modified by gut microbiota and in particular indoles and bile salts.
Institute:University of California, Davis
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258

Subject:

Subject ID:SU000363
Subject Type:Animal
Subject Species:Rattus norvegicus
Taxonomy ID:10116
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA015228AC 8-29_008Control Diet
SA015229AC 9-33_009Control Diet
SA015230AC 10-37_001Control Diet
SA015231AC 4-13_006Control Diet
SA015232AC 7-25_007Control Diet
SA015233AC 11-41_002Control Diet
SA015234AC 2-5_004Control Diet
SA015235AC 12-45_003Control Diet
SA015236AC 3-9_005Control Diet
SA015237HM 8-30_015Resistant Starch
SA015238HM 9-34_016Resistant Starch
SA015239HM 7-26_014Resistant Starch
SA015240HM 2-6_013Resistant Starch
SA015241HM 11-42_011Resistant Starch
SA015242HM 10-38_010Resistant Starch
SA015243HM 12-46_012Resistant Starch
SA015244WW 1-3_029Whole Grain
SA015245WW 12-47_028Whole Grain
SA015246WW 10-39_026Whole Grain
SA015247WW 2-7_030Whole Grain
SA015248WW 8-31_033Whole Grain
SA015249WW 9-35_034Whole Grain
SA015250WW 11-43_027Whole Grain
SA015251WW 7-27_032Whole Grain
SA015252WW 4-15_031Whole Grain
SA015253WR 11-44_018Whole Grain + Resistant Starch
SA015254WR 1-4_020Whole Grain + Resistant Starch
SA015255WR 12-48_019Whole Grain + Resistant Starch
SA015256WR 10-40_017Whole Grain + Resistant Starch
SA015257WR 2-8_021Whole Grain + Resistant Starch
SA015258WR 4-16_022Whole Grain + Resistant Starch
SA015259WR 8-32_024Whole Grain + Resistant Starch
SA015260WR 7-28_023Whole Grain + Resistant Starch
SA015261WR 9-36_025Whole Grain + Resistant Starch
Showing results 1 to 34 of 34

Collection:

Collection ID:CO000357
Collection Summary:Blood collected by heart puncture, anti coagulant and peptidase inhibitor added centrifuged and plasma collected and frozen 70C.
Collection Protocol Filename:StudyDesign-RoyMartin-41415-1.pdf
Sample Type:Serum

Treatment:

Treatment ID:TR000377
Treatment Summary:4 groups: CON = Control Group: Amioca® Starch (100% amylopectin) No RS RS=Test Group: Himaize® High Amylose Starch WG=Control Group: Whole Grain Waxy Flour WG+RS=Test Group: Whole Grain Himaize® Flour (high amylose).
Treatment Protocol Filename:StudyDesign-RoyMartin-41415-1.pdf

Sample Preparation:

Sampleprep ID:SP000370
Sampleprep Summary:1. Switch on bath to pre-cool at –20°C (±2°C validity temperature range) 2. Gently rotate or aspirate the blood samples for about 10s to obtain a homogenised sample. 3. Aliquot 30μl of plasma sample to a 1.0 mL extraction solution. The extraction solution has to be prechilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. 4. Vortex the sample for about 10s and shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. If you are using more than one sample, keep the rest of the sample on ice (chilled at <0°C with sodium chloride). 5. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 450μL portions of the supernatant. One for analysis and one for a backup sample. Store the backup aliquot in -20°C freezer. 7. Evaporate one 450μL aliquots of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. The dried aliquot is then re-suspended with 450 μL 50% acetonitrile (degassed as given above). 9. Centrifuged for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 10. Remove supernatant to a new Eppendorf tube. 11. Evaporate the supernatant to dryness in the Labconco Centrivap cold trap concentrator. 12. Submit to derivatization.

Combined analysis:

Analysis ID AN000555 AN000556
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 6530 Agilent 6550
Column Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak height Peak height

Chromatography:

Chromatography ID:CH000392
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6530
Column Name:Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Sample Injection:1.67 uL
Solvent A:60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid
Solvent B:9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid
Analytical Time:13 min
Capillary Voltage:3500
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase
  
Chromatography ID:CH000393
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6550
Column Name:Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Sample Injection:5.0 uL
Solvent A:60:40 Acetonitrile:Water +10mM Ammonium Acetate +10mM Acetic Acid
Solvent B:9:1 Isopropanol:Acetonitrile +10mM Ammonium Acetate +10mM Acetic Acid
Analytical Time:13 min
Capillary Voltage:3500
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000491
Analysis ID:AN000555
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs
Ion Mode:POSITIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 l/min
Dry Gas Temp:325
Fragment Voltage:120
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Pos
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000492
Analysis ID:AN000556
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are performed in negative and positve mode (two filenames)
Ion Mode:NEGATIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:13 l/min
Dry Gas Temp:200
Fragment Voltage:175
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Neg
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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