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MB Sample ID: SA333661
| Local Sample ID: | SUB13746p4_SPL03 |
| Subject ID: | SU003222 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003222 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SUB13746p4_SPL03 | SA333661 | FL039619 | Vehicle | treatment |
| SUB13746p4_SPL03 | SA333661 | FL039619 | ICC13-7 Xenograft | Sample source |
Collection:
| Collection ID: | CO003215 |
| Collection Summary: | Tumors were collected and snap-frozen in liquid N2 |
| Sample Type: | ICC13-7 xenograft |
Treatment:
| Treatment ID: | TR003231 |
| Treatment Summary: | ICC13-7 xenografts were treated with vehicle vs Pemigatinib(1mg/kg) for 7 days. On the day7, collect tumor 4h after last dose of treatment (vehicle vs 1mg/kg pemigatinib). |
Sample Preparation:
| Sampleprep ID: | SP003228 |
| Sampleprep Summary: | Extractions were conducted following the biphasic extraction protocol. Basically, add cold chloroform to samples (in methanol) with a ratio of 2:1. Vortex samples for 1 minute to homogenize. Add 1 fraction of water, and vortex samples again. Glass vials were centrifuged at 3000 rcf for 10 minutes for phase separation. The aqueous phase was transferred to a new glass vial for metabolomics and the remaining interphase was used for protein quantification. The aqueous phase was evaporated under nitrogen flow. Samples were resuspended in 50% acetonitrile, and the volume was scaled according to the protein amounts. 15ul was used for the lowest biomass, and all others were scaled accordingly. Standard mixes were prepared at 100 uM and run after the samples to allow for the identification of the targets. |
Combined analysis:
| Analysis ID | AN005086 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap ID-X tribrid |
| Ion Mode | UNSPECIFIED |
| Units | area analyzed by Compound Discoverer (counts x seconds) |
Chromatography:
| Chromatography ID: | CH003842 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Temperature: | 40 |
| Flow Gradient: | Started at 93% B/7% A; 40% B/60% A in 19 min; 100% A in 9 min; 100% A for 5 min; back to 93% B/7% A in 3 min and re-equilibration at 93% B/7% A for 9 min. |
| Flow Rate: | 0.05 to 0.15 mL/min in 30 seconds uniformly; then held at 0.15 mL/min. |
| Solvent A: | 100% Water; 20 mMAmmonium Carbonate, 0.1% Ammonium hydroxide |
| Solvent B: | Acetonitrile 97%, 3% water |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004823 |
| Analysis ID: | AN005086 |
| Instrument Name: | Thermo Orbitrap ID-X tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data was acquired on the ID-X in switching polarities at 120000 resolution, with an AGC target of 1e5, and a m/z range of 65 to 1000. MS1 data is acquired in switching polarities for all samples. Data is analyzed in Compound Discoverer 3.3 (CD, ThermoFisher Scientific). A mix of standard of each target was run along the samples and used as the unlabeled reference for the CD labelling workflow. Isotopomer distribution is found in the exchange column, as % of 0 labelled carbon, 1 labelled carbon, 2 labelled carbon, etc. Those are corrected for natural abundance. For the compounds that couldn’t be analyzed by CD, the areas have been extracted with Tracefinder manually. |
| Ion Mode: | UNSPECIFIED |
