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MB Sample ID: SA299532
Local Sample ID: | KPC_CDAKD_4 |
Subject ID: | SU002898 |
Subject Type: | Cultured cells |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Gender: | Not applicable |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002898 |
Subject Type: | Cultured cells |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Gender: | Not applicable |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
KPC_CDAKD_4 | SA299532 | FL036373 | sgCDA | Genotype |
KPC_CDAKD_4 | SA299532 | FL036373 | KPC_FC1245 | Cell Line |
Collection:
Collection ID: | CO002891 |
Collection Summary: | On day 2, cells were harvested on ice by washing them once in ice-cold saline solution (9 g/l NaCl). Cells were covered with 250 μl of pre-cooled 80% methanol for 2 minutes scraped, transferred to fresh vials, and precipitated overnight at -80°C. Then they were centrifuged at 20.009 g for 15min, 4 degrees C and supernatant transferred to an M/S vial. |
Sample Type: | Cultured cells |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR002907 |
Treatment Summary: | Cancer cells were cultured in DMEM medium supplemented with 10% FBS and 1% Pen/Strep in 6-well plates. On day 1, the cells and empty wells (for background noise control), were washed with PBS, and replenished with DMEM containing 10% FBS, 1% Pen/Strep, 5.5 mM glucose, 2 mM glutamine, 1% Pen/Strep, 0.1 mM cytidine (Sigma-Aldrich), or alternately, 0.1 mM labelled cytidine (13C9, 98% 15N3, 96-98%, Eurisotop) for 48h. |
Sample Preparation:
Sampleprep ID: | SP002904 |
Sampleprep Summary: | The samples were centrifuged at 20.000 x g for 15 min at 4°C, supernatant was transferred to appropriate M/S vial for analysis. The cell pellet was dissolved in 100 μl of 200 mM NaOH (for 20 minutes at 95°C), and the protein concentration was determined by using bicinchoninic acid (BCA) reagent method. |
Processing Storage Conditions: | -80℃ |
Extract Storage: | -80℃ |
Combined analysis:
Analysis ID | AN004541 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Waters Acquity |
Column | Waters Acquity UPLC HSS T3 (150 x 2.1mm, 1.8um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap |
Ion Mode | NEGATIVE |
Units | AUC |
Chromatography:
Chromatography ID: | CH003411 |
Chromatography Summary: | C18 IP REVERSE PHASE |
Instrument Name: | Waters Acquity |
Column Name: | Waters Acquity UPLC HSS T3 (150 x 2.1mm, 1.8um) |
Column Temperature: | 40 |
Flow Gradient: | The gradient started with 5% solvent B and 95% solvent A and remained at 5% B until 2min post injection. A linear gradient to 37% B was carried out until 7min and increased to 41% until 14min. Between 14 and 26 minutes the gradient increased to 95% of B and remained at 95% B for 4 minutes. At 30 min the gradient returned to 5% B. The chromatography was stopped at 40 min. |
Flow Rate: | 0.25 mL/min |
Solvent A: | 100% water; 10mM tributylamine; 15mM acetic acid |
Solvent B: | 100% methanol |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS004288 |
Analysis ID: | AN004541 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | EI-Maven polly, ThermoFisher Xcalibur, Metabolites were annotated using the inhouse standard metabolite library- elution time and m/z values. |
Ion Mode: | NEGATIVE |