Summary of Study ST001154

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 PR000773. The data can be accessed directly via it's Project DOI: 10.21228/M8RT1C 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 IDST001154
Study TitleA comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the International Mouse Phenotyping Consortium
Study SummaryUntargeted and targeted metabolomics datasets were acquired for blood plasma samples of 30 mouse knockouts within the International Mouse Phenotyping Consortium (IMPC). http://www.mousephenotype.org/. West Coast Metabolomics Center at UC Davis (https://metabolomics.ucdavis.edu/) conducted the metabolomics analyses.
Institute
University of California, Davis
DepartmentGenome Center
LaboratoryWest Coast Metabolomics Center
Last NameBarupal
First NameDinesh
Address451 East Health Science Drive
Emaildinkumar@ucdavis.edu
Phone5309794354
Submit Date2019-03-12
Num Groups31
Total Subjects220
Num Males110
Num Females110
Raw Data AvailableYes
Raw Data File Type(s)cdf, raw(Thermo), mzML
Analysis Type DetailGC-MS/LC-MS
Release Date2019-04-12
Release Version1
Dinesh Barupal Dinesh Barupal
https://dx.doi.org/10.21228/M8RT1C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000773
Project DOI:doi: 10.21228/M8RT1C
Project Title:A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the International Mouse Phenotyping Consortium
Project Type:Observational study
Project Summary:Untargeted and targeted metabolomics datasets were acquired for blood plasma samples of 30 mouse knockouts and the wildtype strain within the International Mouse Phenotyping Consortium (IMPC http://www.mousephenotype.org/). West Coast Metabolomics Center at UC Davis (https://metabolomics.ucdavis.edu/) conducted the metabolomics analyses.
Institute:University of California, Davis
Department:Genome Center
Last Name:Barupal
First Name:Dinesh
Address:451 Health Science Drive, West Coast Metabolomics Center, Davis, California, 95616, USA
Email:dinkumar@ucdavis.edu
Phone:5309794354

Subject:

Subject ID:SU001238
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:Adult
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Genotype
SA081280215989_027A2m
SA081281204770_025A2m
SA081282216077_028A2m
SA081283204771_026A2m
SA081284216079_029A2m
SA081285216080_030A2m
SA081286190365_065Ahcy
SA081287190372_066Ahcy
SA081288181061_064Ahcy
SA081289180957_062Ahcy
SA081290180958_063Ahcy
SA081291180956_061Ahcy
SA081292123951_017Atp5b
SA081293144064_016Atp5b
SA081294123953_018Atp5b
SA081295143866_013Atp5b
SA081296143869_015Atp5b
SA081297143867_014Atp5b
SA081298296501_122Atp6v0d1
SA081299296503_123Atp6v0d1
SA081300254467_124Atp6v0d1
SA081301254470_126Atp6v0d1
SA081302254468_125Atp6v0d1
SA081303296500_121Atp6v0d1
SA081304224106_041C8a
SA081305222899_040C8a
SA081306257445_039C8a
SA081307257443_038C8a
SA081308224107_042C8a
SA081309233525_037C8a
SA081310217741_113Cdk4
SA081311206819_112Cdk4
SA081312206925_110Cdk4
SA081313206923_109Cdk4
SA081314217742_114Cdk4
SA081315209532_111Cdk4
SA081316125374_053Dhfr
SA081317129283_049Dhfr
SA081318122070_052Dhfr
SA081319129286_051Dhfr
SA081320129285_050Dhfr
SA081321125375_054Dhfr
SA081322424983_127Dync1li1
SA081323447116_132Dync1li1
SA081324447115_131Dync1li1
SA081325428092_130Dync1li1
SA081326424984_128Dync1li1
SA081327427987_129Dync1li1
SA081328410985_088G6pd2
SA081329430037_089G6pd2
SA081330432863_090G6pd2
SA081331420424_085G6pd2
SA081332429932_086G6pd2
SA081333429948_087G6pd2
SA08133443709_043Galc
SA08133540494_047Galc
SA08133643712_045Galc
SA08133740393_046Galc
SA08133843711_044Galc
SA08133940495_048Galc
SA08134038379_094Gnpda1
SA08134140790_095Gnpda1
SA08134240681_092Gnpda1
SA08134340793_096Gnpda1
SA08134438276_091Gnpda1
SA08134540683_093Gnpda1
SA081346190701_012Idh1
SA081347138120_011Idh1
SA081348138110_010Idh1
SA081349115996_009Idh1
SA081350115900_008Idh1
SA081351185262_007Idh1
SA081352435798_023Iqgap1
SA081353487667_024Iqgap1
SA081354506107_022Iqgap1
SA081355493977_021Iqgap1
SA081356487464_019Iqgap1
SA081357487461_020Iqgap1
SA081358111495_100Lmbrd1
SA08135985376_099Lmbrd1
SA08136072465_097Lmbrd1
SA081361118598_101Lmbrd1
SA08136285374_098Lmbrd1
SA081363118599_102Lmbrd1
SA081364225110_035Mfap4
SA081365212480_032Mfap4
SA081366225109_034Mfap4
SA081367212477_031Mfap4
SA081368225111_036Mfap4
SA081369213386_033Mfap4
SA081370356268_074Mmachc
SA081371356157_073Mmachc
SA081372356272_075Mmachc
SA081373356371_076Mmachc
SA081374356475_077Mmachc
SA081375356477_078Mmachc
SA081376349944_156Mvk
SA081377328199_155Mvk
SA081378328195_154Mvk
SA081379345321_152Mvk
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Collection:

Collection ID:CO001232
Collection Summary:Blood specimens were collected using the IMPC protocol https://www.mousephenotype.org/impress/
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001253
Treatment Summary:30 genotypes and one group of wildtype mouse

Sample Preparation:

Sampleprep ID:SP001246
Sampleprep Summary:Metabolites were extracted using standard protocols for GCMS and LCMS assays by the West Coast Metabolomics Center.

Chromatography:

Chromatography ID:CH001408
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC
  
Chromatography ID:CH001409
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Flow Gradient:0 min 85% (A); 0-2 min 70% (A); 2-2.5 min 52% (A); 2.5-11 min 18% (A); 11-11.5 min 1% (A); 11.5-12 min 1% (A); 12-12.1 min 85% (A); 12.1-15 min 85% (A)
Solvent A:Pos mode:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate, Neg mode:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium acetate
Solvent B:Pos mode:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate, Neg mode:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium acetate
Chromatography Type:Reversed phase
  
Chromatography ID:CH001410
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:100% (B) for 2 min, 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min and isocratic until 16.75 min.
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate
Solvent B:95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate
Chromatography Type:HILIC
  
Chromatography ID:CH001411
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:45
Flow Gradient:The 20 min gradient is: 0-0.5 min 10% B, 0.5-1 min 10-20% B, 1-1.5 min 20-22.5% B, 1.5-11 min 22.5-45% B, 11-12.5 min 45-95% B, 12.5-16 min 95% B, 16-16.5 min 95-10% B, 16.5-20 min 10% B
Flow Rate:400 µL/min
Solvent A:100% water; 0.1% formic acid;
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001412
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:45
Flow Gradient:16 min gradient is: 0-1 min 25-40% B, 1-2.5 min 40-42% B, 2.5-4.5 min 42-50% B, 4.5-10.5 min 50-65% B, 10.5-12.5 min 65-75% B, 12.5-14 min 75-85% B, 14-14.5 min 85-95% B, 14.5-15 min 95-25% B, 15-16 min 25% B.
Flow Rate:250 µL/min
Solvent A:100% water; 0.1% acetic acid
Solvent B:90% acetonitrile/10% isopropanol; 0.1% acetic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN001941
Analysis Type:MS
Chromatography ID:CH001408
Num Factors:31
Num Metabolites:128
Units:normalized peak height
  
Analysis ID:AN001942
Analysis Type:MS
Chromatography ID:CH001409
Num Factors:31
Num Metabolites:329
Rt Units:Minutes
Units:normalized peak height
  
Analysis ID:AN001943
Analysis Type:MS
Chromatography ID:CH001409
Num Factors:31
Num Metabolites:223
Rt Units:Minutes
Units:normalized peak height
  
Analysis ID:AN001944
Analysis Type:MS
Chromatography ID:CH001410
Num Factors:31
Num Metabolites:216
Rt Units:Minutes
Units:normalized peak height
  
Analysis ID:AN001945
Analysis Type:MS
Chromatography ID:CH001410
Num Factors:31
Num Metabolites:156
Rt Units:Minutes
Units:normalized peak height
  
Analysis ID:AN001946
Analysis Type:MS
Chromatography ID:CH001411
Num Factors:31
Num Metabolites:91
Rt Units:Minutes
Units:nM
  
Analysis ID:AN001947
Analysis Type:MS
Chromatography ID:CH001412
Num Factors:31
Num Metabolites:64
Rt Units:Minutes
Units:nM
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