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MB Sample ID: SA163998
| Local Sample ID: | SCC-9_3-EV intensity |
| Subject ID: | SU001832 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | SCC-9 and LN1 |
| Cell Strain Details: | Primary tumor (SCC-9) and metastatic (LN1) oral cancer cell lines |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001832 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | SCC-9 and LN1 |
| Cell Strain Details: | Primary tumor (SCC-9) and metastatic (LN1) oral cancer cell lines |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SCC-9_3-EV intensity | SA163998 | FL019539 | Primary tumor EV | Factor |
Collection:
| Collection ID: | CO001825 |
| Collection Summary: | EVs were isolated from SCC-9 and LN1 cell cultures through differential centrifugation. Cells were cultured until 80% cell confluence in 150 mm diameter plates, washed three times with phosphate buffered saline (PBS) and further cultivated for 48 h in media without FBS, at 37°C and 5% CO2. After serum deprivation treatment, the conditioned media (200 mL) was collected and centrifuged at 200 x g for 5 min, 2,000 x g for 15 min, 3,500 x g for 30 min and 10,000 x g for 90 min. The cleared supernatant was further ultracentrifuged at 100,000 x g for 90 min at 4°C and vesicle-containing pellets were washed with PBS by ultracentrifugation for 1.5 h at the same speed. The samples were stored at -80°C until further use. |
| Sample Type: | Keratinocytes |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001845 |
| Treatment Summary: | EVs were not submitted to any treatment prior to metabolites extraction. |
Sample Preparation:
| Sampleprep ID: | SP001838 |
| Sampleprep Summary: | SCC-9 and LN1-derived EVs (5x10e10 particles; 5 biological replicates for each group) were submitted to metabolite extraction using the MTBE method. Derivatization of metabolites was performed as outlined previously (Lisec et al., Nat Protoc. 2015;10(9):1457). |
Combined analysis:
| Analysis ID | AN002859 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890A |
| Column | Agilent DB-35MS (30m x 0,32mm x 0,25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus HT TOF |
| Ion Mode | POSITIVE |
| Units | intensity log2 |
Chromatography:
| Chromatography ID: | CH002117 |
| Instrument Name: | Agilent 7890A |
| Column Name: | Agilent DB-35MS (30m x 0,32mm x 0,25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002652 |
| Analysis ID: | AN002859 |
| Instrument Name: | Leco Pegasus HT TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | GC-TOF-MS data were obtained using a PAL-Combi XT autosampler (PAL System, Switzerland, http://www.palsystem.com/), coupled to an Agilent 7890 A gas chromatograph - Leco Pegasus HT time-of-flight mass spectrometer (LECO, USA) in both split (1:15 and 1:50) and splitless modes (Weckwerth et al., 2004; 101:7809–14). Chromatograms were exported from Leco ChromaTOF software (version 3.25) to R. Peak detection, retention time alignment, and library matching were obtained using the TargetSearch package from Bioconductor (Cuadros-Inostroza et al., BMC Bioinformatics. 2009;10:428). Metabolites were quantified by peak intensity of a selective mass, and metabolite intensities were normalized dividing by the sum of the total ion count followed by log2 transformation. |
| Ion Mode: | POSITIVE |
| Collision Energy: | 70 eV |
