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MB Sample ID: SA193940
| Local Sample ID: | SK2-50K_R10+ |
| Subject ID: | SU002141 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002141 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SK2-50K_R10+ | SA193940 | FL023748 | 4T1-SkM | Genotype |
Collection:
| Collection ID: | CO002134 |
| Collection Summary: | . 4T1-parental and 4T1-SkM cells were plated in 6-well plates at an initial density of 50,000 cells/well and collected 48h later (final density ~275,000 cells/well). Wells were washed twice with 1x PBS and cells were scraped into 1.5 mL microcentrifuge tubes and spun at 16,000 x g for 3 minutes. Samples were then flash frozen and stored at -80°C until ready to process. |
| Sample Type: | Breast cancer cells |
Treatment:
| Treatment ID: | TR002153 |
| Treatment Summary: | A 4T1 subline derived from a rare skeletal muscle metastasis cells was serially passaged through Balb/c mice to achieve a 4T1 derivative that effectively colonized skeletal muscle (termed “4T1-SkM”) |
Sample Preparation:
| Sampleprep ID: | SP002147 |
| Sampleprep Summary: | Prior to LC-MS analysis, tissue samples were weighed and resuspended in pre-chilled (-20°C) methanol:acetonitrile:water (5:3:2, v:v) to a final concentration of 30 mg/ml, cell samples were placed on ice and re-suspended with methanol:acetonitrile:water (5:3:2, v:v) at a concentration of 2x106 cells/mL, and media samples were extracted with the same solution at a dilution of 1:25 (v/v). Suspensions were vortexed continuously for 30 min at 4°C. Insoluble material was removed by centrifugation at 18,000 g for 10 min at 4°C and supernatants were isolated for metabolomics analysis by UHPLC-MS. |
Combined analysis:
| Analysis ID | AN003352 | AN003353 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Phenomenex Kinetex C18 (150 x 2.1mm,2.6um) | Phenomenex Kinetex C18 (150 x 2.1mm,2.6um) |
| 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 | AU | AU |
Chromatography:
| Chromatography ID: | CH002482 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,2.6um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003121 |
| Analysis ID: | AN003352 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 scans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ) |
| Ion Mode: | POSITIVE |
| MS ID: | MS003122 |
| Analysis ID: | AN003353 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 scans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ) |
| Ion Mode: | NEGATIVE |
