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MB Sample ID: SA254625
| Local Sample ID: | TIF_03 |
| Subject ID: | SU002628 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002628 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| TIF_03 | SA254625 | FL032627 | PDAC_TIF | Sample type |
Collection:
| Collection ID: | CO002621 |
| Collection Summary: | Briefly, tumors were rapidly dissected after euthanizing animals. Tumors were weighed and rinsed in blood bank saline solution (150 mM NaCl) and blotted on filter paper (VWR, Radnor, PA, 28298–020). The process of dissection and tumor preparation took < 3min. Tumors were cut in half and put onto 20µm nylon mesh filters (Spectrum Labs, Waltham, MA, 148134) on top of 50 mL conical tubes, and centrifuged for 10min. at 4°C at 400xg. IF was then collected, snap-frozen in liquid nitrogen and stored at -80°C until further analysis. Tumors were then immediately snap frozen using a BioSqueezer (BioSpec) cooled with liquid nitrogen and stored at -80°F until further analysis. |
| Sample Type: | Tumor, Interstitial fluid |
Treatment:
| Treatment ID: | TR002640 |
| Treatment Summary: | Orthotopic tumors were implanted in C57BL6J mice at 8-12 weeks of age. 4 weeks after induction interstitial fluid and tumors were collected. |
Sample Preparation:
| Sampleprep ID: | SP002634 |
| Sampleprep Summary: | Cryogenically frozen tumor pieces were ground to a fine homogenous powder with a liquid nitrogen cooled mortar and pestle. ~30mg of tissue powder was weighed into sample tubes, and metabolites were extracted with 600µL HPLC grade methanol, 300µL HPLC grade water, and 400µL chloroform. Samples were vortexed for 10min at 4°C, centrifuged 21,000xg at 4°C for 10 min. 400µL of the aqueous top layer was removed into a new tube and dried under nitrogen. Dried tumor extracts were resuspended in 100µL HPLC grade water and LC-MS analysis was performed. For TIF samples, we extracted polar metabolites from 5µL of sample using 45µL of a 75:25:0.1 HPLC grade acetonitrile:methanol:formic acid extraction mix. Samples in extraction mix were vortexed for 10 min at 4°C and centrifugated at 15,000x rpm for 10 min at 4°C to pellet insoluble material. 20µL of the soluble polar metabolite supernatant was moved to sample vials for analysis by LC-MS. |
Combined analysis:
| Analysis ID | AN004162 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | Peak area (m/z) |
Chromatography:
| Chromatography ID: | CH003081 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um) |
| Column Temperature: | 25 |
| Flow Gradient: | linear gradient from 80% to 20% B; 20–20.5 min: linear gradient from 20% to 80% B; 20.5–28 min: hold at 80% B |
| Flow Rate: | 0.150 mL/min |
| Solvent A: | 20 mM ammonium carbonate, 0.1% ammonium hydroxide |
| Solvent B: | acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003909 |
| Analysis ID: | AN004162 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | XCalibur 965 2.2 software (Thermo 966 Fisher Scientific) was used for identification and quantification of metabolites. |
| Ion Mode: | UNSPECIFIED |
