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MB Sample ID: SA082454
Local Sample ID: | NaB_3 |
Subject ID: | SU001253 |
Subject Type: | Cultured cells |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001253 |
Subject Type: | Cultured cells |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
NaB_3 | SA082454 | FL012522 | 2 | Time |
NaB_3 | SA082454 | FL012522 | Sodium Butyrate | Treatment |
Collection:
Collection ID: | CO001247 |
Collection Summary: | STHdhQ111 cells were grown on 10cm dishes in triplicate at a seeding density of 1.06 million cells/well. Compound- or vehicle-treated cells were washed with cold 0.9% NaCl. To each 10cm dish of cells, 660uL LC/MS-grade methanol containing internal standards and 330uL LC/MS-grade water were added. Cells were scraped and transferred to Eppendorf tubes, where 450uL chloroform was added. Samples were vortexed at maximum speed (20,817 rcf) for 10 minutes at 4°C. Each layer was collected separately, avoiding the precipitate at the interface of the two layers, and dried by speedvac. |
Sample Type: | Cultured cells |
Treatment:
Treatment ID: | TR001268 |
Treatment Summary: | STHdh cells were incubated in serum-free medium with a compound or vehicle control for 24 hours. |
Sample Preparation:
Sampleprep ID: | SP001261 |
Sampleprep Summary: | For lipid profiling, cells were resuspended in 50uL 60/35/5 acetonitrile/isopropanol/water (v/v/v) and 5uL was injected for LC/MS analysis. For polar metabolite profiling, cells were resuspended in 100uL water and 2uL was injected for LC/MS analysis. |
Combined analysis:
Analysis ID | AN001975 | AN001976 | AN001977 | AN001978 |
---|---|---|---|---|
Analysis type | MS | MS | MS | MS |
Chromatography type | Reversed phase | Reversed phase | HILIC | HILIC |
Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
Column | Ascentis Express C18 (150 x 2.1mm,2.7um) | Ascentis Express C18 (150 x 2.1mm,2.7um) | EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) | EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) |
MS Type | ESI | ESI | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
Units | Peak area | Peak area | Peak Area | Peak Area |
Chromatography:
Chromatography ID: | CH001426 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Ascentis Express C18 (150 x 2.1mm,2.7um) |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH001427 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) |
Chromatography Type: | HILIC |
MS:
MS ID: | MS001829 |
Analysis ID: | AN001975 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | For lipid profiling, cells were resuspended in 50uL 60/35/5 acetonitrile/isopropanol/water (v/v/v) and 5uL was injected for LC/MS analysis. Please see Keckesova et al. and Smulan et al. for a detailed description of the LC/MS analysis (Smulan et al, 2016; Keckesova et al, 2017). Lipid identification and relative quantification was performed using LipidSearch (ThermoFisher Scientific / Mitsui Knowledge Industries). The identified lipids were subjected to quality control filtering and normalization by total signal (Keckesova et al, 2017). |
Ion Mode: | POSITIVE |
MS ID: | MS001830 |
Analysis ID: | AN001976 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | For lipid profiling, cells were resuspended in 50uL 60/35/5 acetonitrile/isopropanol/water (v/v/v) and 5uL was injected for LC/MS analysis. Please see Keckesova et al. and Smulan et al. for a detailed description of the LC/MS analysis (Smulan et al, 2016; Keckesova et al, 2017). Lipid identification and relative quantification was performed using LipidSearch (ThermoFisher Scientific / Mitsui Knowledge Industries). The identified lipids were subjected to quality control filtering and normalization by total signal (Keckesova et al, 2017). |
Ion Mode: | NEGATIVE |
MS ID: | MS001831 |
Analysis ID: | AN001977 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | For polar metabolite profiling, cells were resuspended in 100uL water and 2uL was injected for LC/MS analysis. Please see Birsoy et al. and Chen at al. for a detailed description of the LC/MS analysis (Chen et al, 2016; Birsoy et al, 2015). Untargeted analysis was performed using Progenesis CoMet (Nonlinear Dynamics) using the default settings. Features were filtered based on replicate injections and a dilution series of a pooled sample prepared by mixing equal aliquots of the biological samples. Specifically, the filtering criteria were CV < 0.4 across the four replicate injections and R > 0.9 across a four-point dilution series (comprising 0.1X, 0.3X and 1X concentrations, and a double-volume injection). Features that were not lowest according to the Progenesis quantification in the blank water injection samples were discarded. |
Ion Mode: | POSITIVE |
MS ID: | MS001832 |
Analysis ID: | AN001978 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | For polar metabolite profiling, cells were resuspended in 100uL water and 2uL was injected for LC/MS analysis. Please see Birsoy et al. and Chen at al. for a detailed description of the LC/MS analysis (Chen et al, 2016; Birsoy et al, 2015). Untargeted analysis was performed using Progenesis CoMet (Nonlinear Dynamics) using the default settings. Features were filtered based on replicate injections and a dilution series of a pooled sample prepared by mixing equal aliquots of the biological samples. Specifically, the filtering criteria were CV < 0.4 across the four replicate injections and R > 0.9 across a four-point dilution series (comprising 0.1X, 0.3X and 1X concentrations, and a double-volume injection). Features that were not lowest according to the Progenesis quantification in the blank water injection samples were discarded. |
Ion Mode: | NEGATIVE |