Summary of Study ST000339
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 PR000271. The data can be accessed directly via it's Project DOI: 10.21228/M8RK5G This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000339 |
| Study Title | Metabolites in peritoneal macrophages and bone marrow derived macrophages |
| Study Summary | Experiment looks to identify metabolites in the major metabolic pathways, i.e. glycolysis, tca, urea cycle and ppp along with amino acids. |
| 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 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2015-02-24 |
| Num Groups | 4 |
| Total Subjects | 24 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-06-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000271 |
| Project DOI: | doi: 10.21228/M8RK5G |
| Project Title: | Metabolites in peritoneal macrophages and bone marrow derived macrophages |
| Project Summary: | Experiment looks to identify metabolites in the major metabolic pathways, i.e. glycolysis, tca, urea cycle and ppp along with amino acids. |
| 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: | SU000359 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Subject Comments: | cells |
| Species Group: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA015139 | Quigley_Inj10_SA009 | Bone marrow macrophage |
| SA015140 | Quigley_Inj13_SA010 | Bone marrow macrophage |
| SA015141 | Quigley_Inj04_SA012 | Bone marrow macrophage |
| SA015142 | Quigley_Inj07_SA008 | Bone marrow macrophage |
| SA015143 | Quigley_Inj14_SA011 | Bone marrow macrophage |
| SA015144 | Quigley_Inj06_SA007 | Bone marrow macrophage |
| SA015145 | Quigley_Inj09_SA003 | Resident macrophage |
| SA015146 | Quigley_Inj03_SA002 | Resident macrophage |
| SA015147 | Quigley_Inj08_SA004 | Resident macrophage |
| SA015148 | Quigley_Inj11_SA005 | Resident macrophage |
| SA015149 | Quigley_Inj05_SA006 | Resident macrophage |
| SA015150 | Quigley_Inj12_SA001 | Resident macrophage |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO000353 |
| Collection Summary: | Cells were centrifuged at 500g in PBS, the supernatant aspirated and the cell pellet snap frozen in liquid nitrogen |
| Collection Protocol Filename: | StudyDesign-LauraQuigley-121214.pdf |
| Sample Type: | Cell |
Treatment:
| Treatment ID: | TR000373 |
| Treatment Summary: | Different cell types: 1. Peritoneal macrophages 2. Bone marrow derived macrophages |
| Treatment Protocol Filename: | StudyDesign-LauraQuigley-121214.pdf |
Sample Preparation:
| Sampleprep ID: | SP000366 |
| Sampleprep Summary: | 1. Add 0.5mL of extraction solvent to tube, gently pipet to remove all cells, transfer cells to 2mL eppendorf tube. Repeat for a total of 1mL extraction solvent + cells in 2mL eppendorf tube. 2. Add 2 small stainless steel grinding beads to eppendorf tube 3. Use the GenoGrinder to grind for 3 minutes at 1,250 rpm. 4. Centrifuge at 14,000xg for 5 minutes. 5. Transfer supernatant to a fresh 2mL eppendorf tube. 6. Add 1mL of extraction solvent to tube containing cell pellet + beads, and repeat steps 3 and 4. 7. Collect supernatant, and combine with supernatant collected in step 5. Total volume of extracted sample will be approximately 2mL. 8. Dry down 50uL of extracted sample in 1.5mL eppendorf tube for GC-TOF analysis. 9. Store backups in -20 or -80C. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Yeast_Cells.pdf |
Combined analysis:
| Analysis ID | AN000550 | AN000551 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 6530 | Agilent 6550 |
| 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 height | Peak height |
Chromatography:
| Chromatography ID: | CH000387 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6530 |
| 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% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| 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 |
| Chromatography ID: | CH000388 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6550 |
| 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: | 5.0 uL |
| Solvent A: | 40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM acetic acid; 10mM ammonium acetate |
| 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: | MS000486 |
| Analysis ID: | AN000550 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs Lipidomics runs are performed in negative and positve mode (two filenames) |
| Ion Mode: | POSITIVE |
| 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 |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 |
| 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: | MS000487 |
| Analysis ID: | AN000551 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs Lipidomics runs are performed in negative and positve mode (two filenames) |
| Ion Mode: | NEGATIVE |
| 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 |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
