Summary of study ST000321

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 PR000260. The data can be accessed directly via it's Project DOI: 10.21228/M85S3H This work is supported by NIH grant, U2C- DK119886.

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Study IDST000321
Study TitleEffects of LGG on current drinkers gut metabolism
Study SummaryThis experiment tests the effects of alcoholism by examining the primary metabolites obtained from mouse stool. Stool was collected from 4 groups of mice with varying treatments. One group was not humanized, another was humanized from a healthy human, a third was humanized from a current drinker, and the final group was humanized from a current drinker but also given a treatment of LGG. Humanizations were done to create a model of human gut activity in the mice.
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 Date2014-12-22
Num Groups8
Total Subjects56
Raw Data AvailableYes
Raw Data File Type(s).bin,.xsd,.cd,.cg,.xml
Analysis Type DetailLC-MS
Release Date2016-01-27
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M85S3H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000260
Project DOI:doi: 10.21228/M85S3H
Project Title:Effects of LGG on current drinkers gut metabolism
Project Summary:This experiment tests the effects of alcoholism by examining the primary metabolites obtained from mouse stool. Stool was collected from 4 groups of mice with varying treatments. One group was not humanized, another was humanized from a healthy human, a third was humanized from a current drinker, and the final group was humanized from a current drinker but also given a treatment of LGG. Humanizations were done to create a model of human gut activity in the mice.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
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
Funding Source:U24DK097154

Subject:

Subject ID:SU000341
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA014514ACI7-CCAlcoholic cirrhosis infusion
SA014515ACI9-CCAlcoholic cirrhosis infusion
SA014516ACI6-CCAlcoholic cirrhosis infusion
SA014517ACI1-CCAlcoholic cirrhosis infusion
SA014518ACI8-CCAlcoholic cirrhosis infusion
SA014519ACI5-CCAlcoholic cirrhosis infusion
SA014520ACI3-CCAlcoholic cirrhosis infusion
SA014521ACI4-CCAlcoholic cirrhosis infusion
SA014522ACI2-CCAlcoholic cirrhosis infusion
SA014523CR1-CCGerm Free Control
SA014524CR2-CCGerm Free Control
SA014525CR4-CCGerm Free Control
SA014526CR3-CCGerm Free Control
SA014527LG9-CCLGG Treated
SA014528LG8-CCLGG Treated
SA014529LG6-CCLGG Treated
SA014530LG7-CCLGG Treated
SA014531LG1-CCLGG Treated
SA014532LG2-CCLGG Treated
SA014533LG3-CCLGG Treated
SA014534LG5-CCLGG Treated
SA014535LG4-CCLGG Treated
SA0145366 HIGF-6Normal Human Infusion
SA0145375 HIGF-5Normal Human Infusion
SA0145381 HIGF-1Normal Human Infusion
SA0145392 HIGF-2Normal Human Infusion
SA0145403 HIGF-3Normal Human Infusion
SA0145414 HIGF-4Normal Human Infusion
Showing results 1 to 28 of 28

Collection:

Collection ID:CO000335
Collection Summary:Cecal contents
Collection Protocol Filename:StudyDesign-AvinashSrivastava-82514.pdf
Sample Type:Stool

Treatment:

Treatment ID:TR000355
Treatment Summary:4 treatments: 4 mice who are germ-free (CR1-CC through CR 4 CC) 6 mice who have been humanized with stool from a healthy human (harvested at 30 days) (HI1-LC through HI6-LC) 9 mice who have been humanized with stool from a current drinker(harvested at 30 days) (ACL1-CC through ACL-9-CC) and 9 mice who have been humanized with stool from a current drinker and then supplemented with LGG (harvested at 30 days with 15 days of LGG, LG1-CC through LG9-CC)
Treatment Protocol Filename:StudyDesign_JasBajaj_8414.pdf

Sample Preparation:

Sampleprep ID:SP000349
Sampleprep Summary:Preparation of extraction mix and material before experiment: 1. Switch on bath to pre-cool at –20°C (2°C validity temperature range) 2. Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper 3. Make the extraction solution by missing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 4. Rinse the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation 1. Weigh 50 mg tissue sample in to a 25 ml conical polypropylene centrifuge tube. 2. Add 2.5mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent. 3. Centrifuge the samples at 2500 rpm. for 5 minutes. Aliquot 2 X 500µl supernatant, one for analysis and one for a backup sample. Store backup aliquot in the -20°C freezer. 4. Evaporate one 500µl aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness 5. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 6. Centrifuge for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 7. Remove supernatant to a new Eppendorff tube. 8. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 9. Submit to derivatization.
Sampleprep Protocol Filename:SOP_Extraction_of_Mammalian_Tissue_Samples.pdf

Combined analysis:

Analysis ID AN000510 AN000511
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Unspecified Unspecified
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:CH000359
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Unspecified
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
Internal Standard:See data dictionary
Retention Time:See data dictionary
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:Isopropanol
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000446
Analysis ID:AN000510
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
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000447
Analysis ID:AN000511
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs
Ion Mode:NEGATIVE
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
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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