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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000164 |
| Study Title | Metabolomic analysis of normal and diabetic mouse bone marrow under PBS or metformin treatment |
| Study Type | Untargeted Metabolomics |
| Study Summary | Wild 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 |
| 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 |
| xl15@nyu.edu | |
| Phone | 1-(212)992-7009 |
| Submit Date | 2015-03-04 |
| Num Groups | 4 |
| Total Subjects | 15 samples |
| Study Comments | each sample with 3 technical replicates in each mode |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Uploaded File Size | 7.1 G |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-12-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Mice health condition | Treatment |
|---|---|---|---|
| SA008923 | MKRM1 | MKR | Metformin |
| SA008924 | MKRM3 | MKR | Metformin |
| SA008925 | MKRM2 | MKR | Metformin |
| SA008926 | MKRP4 | MKR | PBS buffer |
| SA008927 | MKRP3 | MKR | PBS buffer |
| SA008928 | MKRP2 | MKR | PBS buffer |
| SA008929 | MKRP1 | MKR | PBS buffer |
| SA008930 | WTM4 | wild type | Metformin |
| SA008931 | WTM3 | wild type | Metformin |
| SA008932 | WTM1 | wild type | Metformin |
| SA008933 | WTM2 | wild type | Metformin |
| SA008934 | WTP4 | wild type | PBS buffer |
| SA008935 | WTP3 | wild type | PBS buffer |
| SA008936 | WTP2 | wild type | PBS buffer |
| SA008937 | WTP1 | wild type | PBS buffer |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO000169 |
| Collection Summary: | - |
| 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 (50 x 4.6mm) | Shodex ODP2 HP-4B 5um polymer (50 x 4.6mm) |
| 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 (50 x 4.6mm) |
| 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/90% water; 10 mM ammonium acetate ; 10 mM acetic acid (positive) or 10 mM NH3.H2O (negative) |
| Solvent B: | 90% acetonitrile/10% water; 10 mM ammonium acetate; 10 mM acetic acid (positive) or 10 mM ammonia (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 |
