Summary of study ST000003

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 PR000003. The data can be accessed directly via it's Project DOI: 10.21228/M8RP44 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000003
Study TitleMetabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells
Study TypeCell Type Comparison
Study Summarymouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis
Institute
University of California, Davis
DepartmentGenome Center
LaboratoryFiehn Laboratory
Last NameMeissen
First NameJohn
Address451 Health Sci Drive, Davis, CA 95616
Emailjkmeissen@ucdavis.edu
Phone530-752-9922
Submit Date2013-01-16
Num Groups3
Total Subjects18
Raw Data AvailableYes
Raw Data File Type(s).xml, .bin, .xsd, .cd,.cG, .mzxml,.sd,.sp
Uploaded File Size5.3 G
Analysis Type DetailLC-MS
Release Date2013-02-15
Release Version1
John Meissen John Meissen
https://dx.doi.org/10.21228/M8RP44
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000003
Project DOI:doi: 10.21228/M8RP44
Project Title:Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells
Project Type:MS study
Institute:University of California, Davis
Department:Genome Center
Laboratory:Fiehn Laboratory
Last Name:Fiehn
First Name:Oliver
Address:451 Health Sci Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:530-754-8258
Funding Source:California Institute for Regenerative Medicine grant RN2-00922, National Institutes of Health grant 1R01GM100782, National Institutes of Health grant R01 DK078328, and National Science Foundation grant MCB-1139644

Subject:

Subject ID:SU000004
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:Embryo
Species Group:Mammal

Factors:

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

mb_sample_id local_sample_id Mouse Cell Line
SA000043m15-T1R1embryonic fibroblast
SA000044m15-T1R2embryonic fibroblast
SA000045m15-T1R3embryonic fibroblast
SA000046m15-T2R1embryonic fibroblast
SA000047m15-T2R2embryonic fibroblast
SA000048m15-T2R3embryonic fibroblast
SA000049mESC-T1R1embryonic stem cell
SA000050mESC-T1R2embryonic stem cell
SA000051mESC-T1R3embryonic stem cell
SA000052mESC-T2R1embryonic stem cell
SA000053mESC-T2R2embryonic stem cell
SA000054mESC-T2R3embryonic stem cell
SA000037iPSC-T1R1iPSC
SA000038iPSC-T1R2iPSC
SA000039iPSC-T1R3iPSC
SA000040iPSC-T2R1iPSC
SA000041iPSC-T2R2iPSC
SA000042iPSC-T2R3iPSC
Showing results 1 to 18 of 18

Collection:

Collection ID:CO000003
Sample Type:Fibroblasts

Treatment:

Treatment ID:TR000005

Sample Preparation:

Sampleprep ID:SP000003
Sampleprep Summary:Cold Methanol Extraction
Processing Method:Homogenization and Solvent Removal w/ Speed Vac
Processing Storage Conditions:On Ice
Extraction Method:3:1 MeOH/H2O
Extract Concentration Dilution:1,000,000 Cells/mL
Extract Storage:-80C
Sample Resuspension:100 uL of 9:1 ACN/H2O with 5mM NH4OAc + 0.2% Acetic Acid
Cell Type:embryonic fibroblasts, embronic stem cells, induced pluripotent stem cells

Combined analysis:

Analysis ID AN000003
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 1290 Infinity
Column Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6530 QTOF
Ion Mode POSITIVE
Units Peak height

Chromatography:

Chromatography ID:CH000003
Chromatography Summary:Untargeted HILIC Method
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Pressure:300 Bar (Max)
Column Temperature:40
Flow Gradient:0-4 min - 0% B, 4-12 min - Gradient to 45% B, 12-20 min - 45% B
Flow Rate:0.25 mL/min
Injection Temperature:4 C
Sample Injection:5 uL
Solvent A:H2O + 5mM NH4OAc + 0.2% Acetic Acid
Solvent B:9:1 Acetonitrile:H2O + 5mM NH4OAc + 0.2% Acetic Acid
Analytical Time:20 min
Chromatography Type:HILIC

MS:

MS ID:MS000003
Analysis ID:AN000003
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Collision Energy:Ramped - 0.02eV/m/z + 10 eV
Collision Gas:N2
Dry Gas Flow:Neb - 10 L/min, Sheath 9 L/min
Dry Gas Temp:Neb/Sheath - 350C
Gas Pressure:35 PSI
Ionization:Electrospray Ionization
Mass Accuracy:<1.5 mDa
Dataformat:.d
Scan Range Moverz:100-1700
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