Summary of study ST000075

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 PR000054. The data can be accessed directly via it's Project DOI: 10.21228/M87G65 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000075
Study TitleCombined Metabolomics and Lipidomics of Type 1 Diabetes (QTOF)
Study Typebiomarker study
Study SummaryThis West Coast Metabolomics Center pilot and feasibility project granted to Graeme Bell  (University of Chicago) and collaborator Manami Hara uses a multi-omics approach to investigate the metabolome (primary metabolites), lipidome (complex lipids) and signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice which progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice (n=71) were assessed as diabetic or non-diabetic based on their fasting (4hr) blood glucose levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and 41 normoglycemic animals. The primary objective of this study was to identify candidate biomarkers associated with beta-cell destruction/survival and T1D progression.
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 Date2014-06-11
Num Groups2
Total Subjects71
Study CommentsLipidomics profiles for study
Raw Data AvailableYes
Raw Data File Type(s).cd,.cG,.stG,.xml, .bin,.xsd
Uploaded File Size52 G
Analysis Type DetailLC-MS
Release Date2014-07-23
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M87G65
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000054
Project DOI:doi: 10.21228/M87G65
Project Title:Combined Metabolomics and Lipidomics of Type 1 Diabetes
Project Type:MS study
Project Summary:This West Coast Metabolomics Center pilot and feasibility project granted to Graeme Bell  (University of Chicago) and collaborator Manami Hara uses a multi-omics approach to investigate the metabolome (primary metabolites), lipidome (complex lipids) and signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice which progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice (n=71) were assessed as diabetic or non-diabetic based on their fasting (4hr) blood glucose levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and 41 normoglycemic animals. The primary objective of this study was to identify candidate biomarkers associated with beta-cell destruction/survival and T1D progression.
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:NIH U24DK097154

Subject:

Subject ID:SU000094
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 Diagnosis
SA003890Inj052_Manami_56_CSHMS_6530B.ddiabetic
SA003891Inj071_Manami_57_CSHMS_6530B.ddiabetic
SA003892Inj011_Manami_55_CSHMS_6530B.ddiabetic
SA003893Inj069_Manami_60_CSHMS_6530B.ddiabetic
SA003894Inj019_Manami_53_CSHMS_6530B.ddiabetic
SA003895Inj035_Manami_54_CSHMS_6530B.ddiabetic
SA003896Inj012_Manami_73_CSHMS_6530B.ddiabetic
SA003897Inj054_Manami_4_CSHMS_6530B.ddiabetic
SA003898Inj006_Manami_76_CSHMS_6530B.ddiabetic
SA003899Inj004_Manami_52_CSHMS_6530B.ddiabetic
SA003900Inj056_Manami_67_CSHMS_6530B.ddiabetic
SA003901Inj020_Manami_62_CSHMS_6530B.ddiabetic
SA003902Inj010_Manami_63_CSHMS_6530B.ddiabetic
SA003903Inj017_Manami_13_CSHMS_6530B.ddiabetic
SA003904Inj033_Manami_17_CSHMS_6530B.ddiabetic
SA003905Inj036_Manami_19_CSHMS_6530B.ddiabetic
SA003906Inj055_Manami_12_CSHMS_6530B.ddiabetic
SA003907Inj048_Manami_10_CSHMS_6530B.ddiabetic
SA003908Inj063_Manami_6_CSHMS_6530B.ddiabetic
SA003909Inj043_Manami_49_CSHMS_6530B.ddiabetic
SA003910Inj003_Manami_7_CSHMS_6530B.ddiabetic
SA003911Inj050_Manami_20_CSHMS_6530B.ddiabetic
SA003912Inj039_Manami_15_CSHMS_6530B.ddiabetic
SA003913Inj061_Manami_36_CSHMS_6530B.ddiabetic
SA003914Inj068_Manami_37_CSHMS_6530B.ddiabetic
SA003915Inj030_Manami_47_CSHMS_6530B.ddiabetic
SA003916Inj058_Manami_32_CSHMS_6530B.ddiabetic
SA003917Inj005_Manami_40_CSHMS_6530B.ddiabetic
SA003918Inj062_Manami_25_CSHMS_6530B.ddiabetic
SA003919Inj064_Manami_30_CSHMS_6530B.ddiabetic
SA003920Inj037_Manami_46_CSHMS_6530B.dnon-diabetic
SA003921Inj049_Manami_48_CSHMS_6530B.dnon-diabetic
SA003922Inj018_Manami_50_CSHMS_6530B.dnon-diabetic
SA003923Inj066_Manami_45_CSHMS_6530B.dnon-diabetic
SA003924Inj024_Manami_43_CSHMS_6530B.dnon-diabetic
SA003925Inj007_Manami_51_CSHMS_6530B.dnon-diabetic
SA003926Inj023_Manami_41_CSHMS_6530B.dnon-diabetic
SA003927Inj060_Manami_42_CSHMS_6530B.dnon-diabetic
SA003928Inj051_Manami_44_CSHMS_6530B.dnon-diabetic
SA003929Inj041_Manami_69_CSHMS_6530B.dnon-diabetic
SA003930Inj034_Manami_66_CSHMS_6530B.dnon-diabetic
SA003931Inj067_Manami_68_CSHMS_6530B.dnon-diabetic
SA003932Inj009_Manami_39_CSHMS_6530B.dnon-diabetic
SA003933Inj070_Manami_65_CSHMS_6530B.dnon-diabetic
SA003934Inj032_Manami_64_CSHMS_6530B.dnon-diabetic
SA003935Inj008_Manami_59_CSHMS_6530B.dnon-diabetic
SA003936Inj042_Manami_61_CSHMS_6530B.dnon-diabetic
SA003937Inj045_Manami_58_CSHMS_6530B.dnon-diabetic
SA003938Inj022_Manami_14_CSHMS_6530B.dnon-diabetic
SA003939Inj053_Manami_11_CSHMS_6530B.dnon-diabetic
SA003940Inj047_Manami_16_CSHMS_6530B.dnon-diabetic
SA003941Inj027_Manami_18_CSHMS_6530B.dnon-diabetic
SA003942Inj021_Manami_21_CSHMS_6530B.dnon-diabetic
SA003943Inj031_Manami_9_CSHMS_6530B.dnon-diabetic
SA003944Inj038_Manami_8_CSHMS_6530B.dnon-diabetic
SA003945Inj057_Manami_1_CSHMS_6530B.dnon-diabetic
SA003946Inj001_Manami_2_CSHMS_6530B.dnon-diabetic
SA003947Inj044_Manami_3_CSHMS_6530B.dnon-diabetic
SA003948Inj015_Manami_5_CSHMS_6530B.dnon-diabetic
SA003949Inj014_Manami_22_CSHMS_6530B.dnon-diabetic
SA003950Inj026_Manami_23_CSHMS_6530B.dnon-diabetic
SA003951Inj016_Manami_31_CSHMS_6530B.dnon-diabetic
SA003952Inj025_Manami_33_CSHMS_6530B.dnon-diabetic
SA003953Inj029_Manami_34_CSHMS_6530B.dnon-diabetic
SA003954Inj028_Manami_35_CSHMS_6530B.dnon-diabetic
SA003955Inj013_Manami_29_CSHMS_6530B.dnon-diabetic
SA003956Inj059_Manami_28_CSHMS_6530B.dnon-diabetic
SA003957Inj046_Manami_24_CSHMS_6530B.dnon-diabetic
SA003958Inj040_Manami_26_CSHMS_6530B.dnon-diabetic
SA003959Inj002_Manami_27_CSHMS_6530B.dnon-diabetic
SA003960Inj065_Manami_38_CSHMS_6530B.dnon-diabetic
SA003887Biorec3_CSHMS_6530B.dQC - quality check sample
SA003888Biorec4_CSHMS_6530B.dQC - quality check sample
SA003889Biorec1_CSHMS_6530B.dQC - quality check sample
Showing results 1 to 74 of 74

Collection:

Collection ID:CO000077
Collection Protocol Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
Sample Type:Blood

Treatment:

Treatment ID:TR000095
Treatment Protocol Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf

Sample Preparation:

Sampleprep ID:SP000090
Sampleprep Protocol Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf

Combined analysis:

Analysis ID AN000119 AN000120
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
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 area Peak area

Chromatography:

Chromatography ID:CH000081
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
Instrument Name:Waters Acquity
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:Same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000095
Analysis ID:AN000119
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
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
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:MS000096
Analysis ID:AN000120
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
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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