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MB Sample ID: SA078790
Local Sample ID: | HCC2279_LUNG |
Subject ID: | SU001206 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001206 |
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 |
---|---|---|---|---|
HCC2279_LUNG | SA078790 | FL012063 | lung_NSC | Classifications |
HCC2279_LUNG | SA078790 | FL012063 | RPMI 1640 + 10% FBS | Cell Culture Media |
Collection:
Collection ID: | CO001200 |
Collection Summary: | Cancer Cell Line Encyclopedia: a collection of 928 cancer cell lines |
Sample Type: | Cultured cells |
Treatment:
Treatment ID: | TR001221 |
Treatment Summary: | No treatment applied to cells |
Sample Preparation:
Sampleprep ID: | SP001214 |
Sampleprep Summary: | Polar metabolite extraction LC-MS grade solvents were used for all of the metabolite extraction in this study. For adherent cells, the media were aspirated off as much as possible and the cells were washed with 4 mL cold Phosphate Buffered Saline (PBS, no Mg2+/Ca2+). After vacuum aspiration of PBS, the metabolites were extracted by adding 4 mL 80% methanol (-80°C) immediately and the samples were transferred to a -80°C freezer. The flasks were kept on dry ice during the transfer and were incubated at -80°C for 15 min. Then the lysate was collected by a cell scraper and transferred to a 15 mL conical tube on dry ice. The insoluble debris was removed by centrifuging at 3500 rpm for 10 min (4°C). The supernatant was transferred to a new 15 mL conical tube on dry ice and the tube with the pellet was kept for further extraction. Then, 500 μL 80% methanol (-80°C) was added to each pellet. The mixture was resuspended by vortexing or pipetting and transferred to a 1.5 ml centrifuge tube on dry ice. The cell debris was removed by centrifuging samples at 10,000 rpm for 5 min (4°C). The supernatant was transferred to the corresponding 15 mL conical tube on dry ice so that all extracts were combined. The pooled extracts were stored at - 80°C before LC-MS analysis. For cells growing in suspension, they were centrifuged to pellet at 300g for 5 min (4°C) and the supernatant was then aspirated off as much as possible. These cells were washed once with 4 mL cold PBS (no Mg2+/Ca2+) and they were pelleted at 300g for 5 min (4°C). After vacuum aspiration of PBS, the metabolites were extracted by adding 4 mL 80% methanol (-80°C) immediately and the samples were transferred to a -80°C freezer after brief vortexing. The samples were kept on dry ice during the transfer and were incubated at -80°C for 15 min. The insoluble debris was removed by centrifuging at 3500 rpm for 10 min (4°C). The subsequent steps were the same as those used for adherent cell lines Lipid extraction For adherent cells, the medium was aspirated off as much as possible and the cells were washed with 4 mL cold PBS (no Mg2+/Ca2+). After vacuum aspiration of PBS, the lipid metabolites were extracted by adding 4 mL isopropanol (4°C) and the lysate was collected by a cell scraper and transferred to a 15 mL conical tube on ice. The samples were covered to avoid exposure to light and were allowed to sit for 1h at 4°C. Samples were then vortexed and the cell debris was removed by centrifuging at 3500 rpm for 10 min (4°C). The supernatant was transferred to a new 15 mL centrifuge tube on ice and stored at -20°C before LC-MS analysis. For cells growing in suspension, they were centrifuged to pellet at 300g for 5 min (4°C) and the supernatant was then aspirated off as much as possible. These cells were washed once with 4 mL cold PBS (no Mg2+/Ca2+) and they were pelleted at 300g for 5 min (4°C). After vacuum aspiration of PBS, the lipid metabolites were extracted by adding 4 mL isopropanol (4°C) immediately. After brief vortexing, the samples were covered to avoid exposure to light and were allowed to sit for 1h at 4°C. The insoluble debris was removed by centrifuging at 3500 rpm for 10 min (4°C). The supernatant was transferred to a new 15 mL centrifuge tube on ice and stored at -20°C before LC-MS analysis. |
Combined analysis:
Analysis ID | AN001875 | AN001876 | AN001877 |
---|---|---|---|
Analysis type | MS | MS | MS |
Chromatography type | HILIC | HILIC | Reversed phase |
Chromatography system | Agilent 1100 | Waters Acquity | Agilent 1200 |
Column | Unspecified | Phenomenex Luna NH2 (150 x 2.1mm,3um) | Unspecified |
MS Type | ESI | ESI | ESI |
MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole |
MS instrument name | ABI Sciex 4000 QTrap | ABI Sciex 5500 QTrap | ABI Sciex 4000 QTrap |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE |
Units | Abundances | Abundances | Abundances |
Chromatography:
Chromatography ID: | CH001356 |
Chromatography Summary: | HILIC-pos |
Instrument Name: | Agilent 1100 |
Column Name: | Unspecified |
Chromatography Type: | HILIC |
Chromatography ID: | CH001357 |
Chromatography Summary: | HILIC-neg |
Instrument Name: | Waters Acquity |
Column Name: | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
Chromatography Type: | HILIC |
Chromatography ID: | CH001358 |
Chromatography Summary: | C4-pos |
Instrument Name: | Agilent 1200 |
Column Name: | Unspecified |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS001731 |
Analysis ID: | AN001875 |
Instrument Name: | ABI Sciex 4000 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | n/a |
Ion Mode: | POSITIVE |
MS ID: | MS001732 |
Analysis ID: | AN001876 |
Instrument Name: | ABI Sciex 5500 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | n/a |
Ion Mode: | NEGATIVE |
MS ID: | MS001733 |
Analysis ID: | AN001877 |
Instrument Name: | ABI Sciex 4000 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | Full scan data were acquired using Q1 scanning |
Ion Mode: | POSITIVE |