Summary of study ST000164

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 PR000142. The data can be accessed directly via it's Project DOI: 10.21228/M8MG6K This work is supported by NIH grant, U2C- DK119886.

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Study IDST000164
Study TitleMetabolomic analysis of normal and diabetic mouse bone marrow under PBS or metformin treatment
Study TypeUntargeted Metabolomics
Study SummaryWild type and diabetic (MKR) mice were treated daily with intraperitoneal injections of 50 microliters of PBS (control) or metformin (200 mg/kg body weight) for 14 days. Their bone marrow cells were collected and compared by untargeted metabolomics.
Institute
New York University
DepartmentCollege of Dentistry, Basic Science and Craniofacial Biology
LaboratoryXin Li Laboratory
Last NameXin
First NameLi
Address345 East 24th Street, Room 901D, New York, NY 10010
Emailxl15@nyu.edu
Phone1-(212)992-7009
Submit Date2015-03-04
Num Groups4
Total Subjects15 samples
Study Commentseach sample with 3 technical replicates in each mode
Raw Data AvailableYes
Raw Data File Type(s).raw
Uploaded File Size7.1 G
Analysis Type DetailLC-MS
Release Date2016-12-22
Release Version1
Li Xin Li Xin
https://dx.doi.org/10.21228/M8MG6K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000142
Project DOI:doi: 10.21228/M8MG6K
Project Title:Bone marrow metabolomics of MKR mice under metformin treatment
Project Type:Untargeted Metabolomics on metformin responses in bone marrows of diabetic mice
Institute:New York University
Department:College of Dentistry, Basic Science and Craniofacial Biology
Laboratory:Xin Li Laboratory
Last Name:Xin
First Name:Li
Address:345 East 24th Street, Room 901D, New York, NY 10010
Email:xl15@nyu.edu
Phone:1-(212)992-7009
Funding Source:NIH grants R01CA180277, CA172894, 5R01GM06248012-12, NIDDK grant 3U54DK10255602S2, California Institute for Regenerative Medicine grant RB4-06087.

Subject:

Subject ID:SU000183
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:FVB (wild type)|MKR (FVB background)
Age Or Age Range:12 week old|12 week old
Gender:male|male
Animal Animal Supplier:JAX lab|LeRoith laboratory
Species Group:Mammal

Factors:

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

mb_sample_id local_sample_id Mice health condition Treatment
SA008923MKRM1MKR Metformin
SA008924MKRM3MKR Metformin
SA008925MKRM2MKR Metformin
SA008926MKRP4MKR PBS buffer
SA008927MKRP3MKR PBS buffer
SA008928MKRP2MKR PBS buffer
SA008929MKRP1MKR PBS buffer
SA008930WTM4wild type Metformin
SA008931WTM3wild type Metformin
SA008932WTM1wild type Metformin
SA008933WTM2wild type Metformin
SA008934WTP4wild type PBS buffer
SA008935WTP3wild type PBS buffer
SA008936WTP2wild type PBS buffer
SA008937WTP1wild type PBS buffer
Showing results 1 to 15 of 15

Collection:

Collection ID:CO000169
Collection Protocol Filename:Protocol_Methods_metformin_Li.pdf
Sample Type:total bone marrow flush (cells)
Storage Conditions:-20°C

Treatment:

Treatment ID:TR000189
Treatment:abiotic
Treatment Compound:metformin
Treatment Route:Intraperitoneal injection
Treatment Dose:200 mg/kg body weight
Treatment Dosevolume:50 microliters
Treatment Doseduration:daily for 14 days
Treatment Vehicle:phosphate buffered solution

Sample Preparation:

Sampleprep ID:SP000183
Sampleprep Summary:Frozen cells were mixed with dry ice-cool 80% methanol (mass-spec grade) at a ratio of 30 ?L/million cells, and then quickly thawed on heat block set at 50 °C for 5 min. The suspension was then processed by three rounds of 1 min vortex at max speed, chilled briefly on dry ice. The mixture was incubated at 4°C for 1 hour before centrifuge at 20,000 x g for 20 min at 4 °C. The supernatant was stored at -20 °C and used as metabolite extract for LC-MS analysis.
Sampleprep Protocol Filename:Protocol_Methods_metformin_Li.pdf
Processing Method:Homogenization and Centrifugation
Processing Storage Conditions:On ice
Extraction Method:80% Methanol
Extract Concentration Dilution:30 microliters solvent per million cells
Extract Storage:-20°C
Cell Type:bone marrow

Combined analysis:

Analysis ID AN000256 AN000257
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Exactive Thermo Exactive
Column Shodex ODP2 HP-4B 5um polymer 4.6 x 50 mm Shodex ODP2 HP-4B 5um polymer 4.6 x 50 mm
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH000181
Chromatography Summary:Untarged mix-mode method
Instrument Name:Thermo Exactive
Column Name:Shodex ODP2 HP-4B 5um polymer 4.6 x 50 mm
Column Pressure:150 Bar (Max)
Column Temperature:45
Flow Gradient:0-15 min -1% B, 15-19 min- gradient 1 to 99% B, 18-24 min- 99% B, 24-25 min-gradient 99% to 1% B, 25-30 min-1% B
Flow Rate:0.1 ml/min
Injection Temperature:4 C
Sample Injection:5 uL
Solvent A:10% Acetonitrile + 10 mM NH4OAc + 10 mM Acetic acid (positive) or 10 mM NH3.H2O (negative)
Solvent B:90% Acetonitrile + 10 mM NH4OAc + 10 mM Acetic acid (positive) or 10 mM NH3.H2O (negative)
Analytical Time:30 min
Capillary Voltage:3.5 kv (positive), 3.1 kv (negative)
Transferline Temperature:275C
Washing Buffer:10% Acetonitrile
Weak Wash Solvent Name:10% Acetonitrile
Weak Wash Volume:600 uL
Strong Wash Solvent Name:90% Acetonitrile
Strong Wash Volume:200 uL
Sample Loop Size:20 uL
Chromatography Type:Reversed phase

MS:

MS ID:MS000206
Analysis ID:AN000256
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:30V
Collision Gas:40 units
Ion Source Temperature:3.5 kv
Ion Spray Voltage:Electrospray Ionization
Ionization Potential:< 2ppm
Atom Gun Current:3000000
Sample Dripping:75-1200
Scanning Range:20 v
Skimmer Voltage:120 v
  
MS ID:MS000207
Analysis ID:AN000257
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:30V
Collision Gas:40 units
Ion Source Temperature:3.1 kv
Ion Spray Voltage:Electrospray Ionization
Ionization Potential:< 4 ppm
Atom Gun Current:3000000
Sample Dripping:75-1200
Scanning Range:20 v
Skimmer Voltage:120 v
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