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MB Sample ID: SA185696
| Local Sample ID: | OUHSC-10 |
| Subject ID: | SU002064 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
| Cell Biosource Or Supplier: | OVCAR4 cell line was obtained from Dr. Thomas Hamilton (Fox Chase Cancer Center, PA) and OVCAR8 cells were from National Cancer Institute (NCI). Kuramochi, TYKNU, OVKATE and OVSAHO cell lines were from the JCRB Cell Bank, Tokyo, Japan. SNU119, SNU251, ES-2, OVCAR3, CAOV3 and OV90 cells were from Seoul National University, Seoul, Korea, and COV362, OAW28 and COV318 cells were purchased from Sigma-Aldrich (St. Louis, MO). |
| Cell Passage Number: | 3 and 4 |
| Cell Counts: | 20 million cells |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002064 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
| Cell Biosource Or Supplier: | OVCAR4 cell line was obtained from Dr. Thomas Hamilton (Fox Chase Cancer Center, PA) and OVCAR8 cells were from National Cancer Institute (NCI). Kuramochi, TYKNU, OVKATE and OVSAHO cell lines were from the JCRB Cell Bank, Tokyo, Japan. SNU119, SNU251, ES-2, OVCAR3, CAOV3 and OV90 cells were from Seoul National University, Seoul, Korea, and COV362, OAW28 and COV318 cells were purchased from Sigma-Aldrich (St. Louis, MO). |
| Cell Passage Number: | 3 and 4 |
| Cell Counts: | 20 million cells |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| OUHSC-10 | SA185696 | FL022964 | No treatment | Treatment |
Collection:
| Collection ID: | CO002057 |
| Collection Summary: | Immortalized normal fallopian-tube-derived epithelial cells (FTE188) have been previously described and used here (1). High grade serous carcinoma cell line OVCAR3, OVCAR8, OVKATE, SNU119, SNU251, OVCAR4, OVSAHO, and Kuramochi cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Cellgro, Manassas, VA), COV362, COV318, OAW28 and CAOV3 cells were maintained in Dulbecco’s modified Eagle’s (DMEM) Medium (Cellgro, Manassas, VA). OV90 cells were maintained in MCDB105: M199 (1:1) Medium (Thermo Fisher Scientific, Waltham, MA) and TYKNU cells were maintained in Minimum Essential Medium (MEM) (Cellgro, Manassas, VA). ES-2 cells were maintained in McCoy’s 5A medium (Sigma-Aldrich, St. Louis, MO). All cells were maintained at 37°C in a 5% CO2 incubator. All media were supplemented with 10% FBS (Gemini Bio-Products, West Sacramento, CA), 50 U/mL penicillin, 50 μg/ml streptomycin (Cellgro, Manassas, VA). Cells were grown to 20 million cells and washed with cold PBS. Cells were collected by scraping them off the plates. |
| Sample Type: | Ovarian cancer cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002076 |
| Treatment Summary: | No treatment was done. |
Sample Preparation:
| Sampleprep ID: | SP002070 |
| Sampleprep Summary: | Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. In order to dissociate small molecules bound to or trapped in proteins, lysate was precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN003234 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters ACQUITY ultra-performance liquid chromatography (UPLC) |
| Column | Waters UPLC BEH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | ratio |
Chromatography:
| Chromatography ID: | CH002385 |
| Instrument Name: | Waters ACQUITY ultra-performance liquid chromatography (UPLC) |
| Column Name: | Waters UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003008 |
| Analysis ID: | AN003234 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Raw data files are archived and extracted using proprietary, Metabolon LIMS data structures and analysis software (Metabolon Inc, Durham). Briefly, raw data was extracted, peak-identified and QC processed using Metabolon’s hardware and software. Biochemical identifications are based on three criteria: retention index within a narrow RI window of the proposed identification, accurate mass match to the library +/- 10 ppm, and the MS/MS forward and reverse scores between the experimental data and authentic standards. |
| Ion Mode: | UNSPECIFIED |
