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MB Sample ID: SA162631
Local Sample ID: | control3 |
Subject ID: | SU001808 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001808 |
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 |
---|---|---|---|---|
control3 | SA162631 | FL019214 | Control | Factor |
Collection:
Collection ID: | CO001801 |
Collection Summary: | MCF7 cells were purchased from American Type Culture Collection (ATCC). All cancer cell lines were maintained in RPMI 1640 (Sigma R8758) containing glucose (2 mg/ml) and glutamine (0.6 mg/ml) but no pyruvate and was supplemented with 5% Fetal calf serum. |
Sample Type: | Cultured cells |
Treatment:
Treatment ID: | TR001821 |
Treatment Summary: | MCF7 cell transfections were performed using siPORT NeoFX Transfection Agent (ThermoFisher Scientific) following the recommended protocol for an oligonucleotide siRNA based on the previously described MCJ targeting sequence. |
Sample Preparation:
Sampleprep ID: | SP001814 |
Sampleprep Summary: | All cancer cell lines were maintained in RPMI 1640 (Sigma R8758) containing glucose (2 mg/ml) and glutamine (0.6 mg/ml) but no pyruvate and was supplemented with 5% Fetal calf serum. Metabolic profile comparisons of cells were performed on equal cell numbers. Cells were cultured under normal conditions, detached using trypsin-EDTA (0.05 %), counted, normalized to 0.5 x 10e6 in each sample, and cell pellets were snap frozen in liquid nitrogen prior to analysis. Briefly, 2 x 10e6 cells and 20μL cell media were extracted in 1mL and 980μL cold lysis and extraction buffer (methanol : acetonitrile : water, 5:3:2), respectively, and pellets were discarded. |
Combined analysis:
Analysis ID | AN002817 | AN002818 |
---|---|---|
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 | Relative Abundance | Relative Abundance |
Chromatography:
Chromatography ID: | CH002082 |
Chromatography Summary: | Positive Mode 10 μL of water and methanol soluble fractions were run through a Kinetex C18 1.7 μm, 100 x 2.1 mm (Phenomenex) reversed phase column (Positive ion mode - phase A: water, 0.1 % formic acid; B: acetonitrile, 0.1 % formic acid) via an ultra-high performance chromatographic system (UHPLC - Vanquish, Thermo Fisher). UHPLC was coupled in line with a high-resolution quadrupole Orbitrap instrument run in positive polarity mode (QExactive, Thermo Fisher) at 70,000 resolution (at 200 m/z). Gradients and other technical parameters and the variants employed herein have been extensively described. |
Instrument Name: | Thermo Vanquish |
Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,2.6um) |
Solvent A: | 100% water; 0.1 % formic acid |
Solvent B: | 100% acetonitrile, 0.1 % formic acid |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH002083 |
Chromatography Summary: | Negative Mode 10 μL of water and methanol soluble fractions were run through a Kinetex C18 1.7 μm, 100 x 2.1 mm (Phenomenex) reversed phase column (Negative ion mode – phase A: 1 mM NH4Ac 95:5 water : acetonitrile; phase B: 1 mM NH4Ac 95:5 acetonitrile : water) via an ultra-high performance chromatographic system (UHPLC - Vanquish, Thermo Fisher). UHPLC was coupled in line with a high-resolution quadrupole Orbitrap instrument run in negative polarity mode (QExactive, Thermo Fisher) at 70,000 resolution (at 200 m/z). Gradients and other technical parameters and the variants employed herein have been extensively described. |
Instrument Name: | Thermo Vanquish |
Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,2.6um) |
Solvent A: | 95% water/5% acetonitrile; 1 mM ammonium acetate |
Solvent B: | 95% acetonitrile/5% water; 1 mM ammonium acetate |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS002611 |
Analysis ID: | AN002817 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | UHPLC was coupled in line with a high-resolution quadrupole Orbitrap instrument run in positive polarity mode (QExactive, Thermo Fisher) at 70,000 resolution (at 200 m/z). Gradients and other technical parameters and the variants employed herein have been extensively described. |
Ion Mode: | POSITIVE |
MS ID: | MS002612 |
Analysis ID: | AN002818 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | UHPLC was coupled in line with a high-resolution quadrupole Orbitrap instrument run in negative polarity mode (QExactive, Thermo Fisher) at 70,000 resolution (at 200 m/z). Gradients and other technical parameters and the variants employed herein have been extensively described. |
Ion Mode: | NEGATIVE |