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MB Sample ID: SA160362
Local Sample ID: | 4203 |
Subject ID: | SU001789 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Age Or Age Range: | 6–8 weeks old |
Gender: | Female |
Animal Animal Supplier: | Charles River Frederick Research Model Facility |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001789 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Age Or Age Range: | 6–8 weeks old |
Gender: | Female |
Animal Animal Supplier: | Charles River Frederick Research Model Facility |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
4203 | SA160362 | FL018802 | RT | Treatment |
4203 | SA160362 | FL018802 | RT+24 | Time |
4203 | SA160362 | FL018802 | RT | Treatment |
4203 | SA160362 | FL018802 | RT+24 | Time |
Collection:
Collection ID: | CO001782 |
Collection Summary: | Blood was collected approximately every 10 days from the tail vein of the mice in Li-heparin collection tubes and immediately processed to separate plasma. |
Sample Type: | Blood (plasma) |
Treatment:
Treatment ID: | TR001802 |
Treatment Summary: | Radiation was performed on mice intracranially injected with the NCH1681 cell line. Mice were irradiated with a total of 12Gy; specifically, animals were treated on Monday and Friday for 2 consecutive weeks at 3Gy/session. Radiation was performed in a Pantek machine an orthovoltage radiotherapy unit. The mice were anesthetized with a cocktail of ketamine/rompun/saline mixture, i.e. ketamine (100mg/ml), rompun (20mg/ml) and diluted with saline to give the mice a 100mg/kg dose of ketamine and 10mg/kg rompun. The mice were injected with the cocktail at a dose of 0.01 µL per gram of half of the mouse’s body weight. Animals were then placed in a custom-made jig. During radiation, lead shielding covered the eyes, ears, the oral cavity, and the spinal cord. After radiation, the mice were given atipamezole, a reversal agent, to aid in the recovery. |
Sample Preparation:
Sampleprep ID: | SP001795 |
Sampleprep Summary: | Blood samples were separated into plasma and packed cells by centrifugation at 3,500g for 15 min at 4°C and stored at -80°C until extraction. 35 µL of plasma were extracted in a water:methanol:chloroform mixture. Centrifuged for 20 min at 4°ᵒC and 13,000 rpm and the resulting upper hydrophilic phase was then transferred to a clean vial and dried under a stream of N2 gas. Dried sediments were resuspended in 60% methanol (aq.) and injected into the LCMS system. |
Combined analysis:
Analysis ID | AN002787 |
---|---|
Analysis type | MS |
Chromatography type | HILIC |
Chromatography system | Agilent 6545 QTOF-MS |
Column | AdvanceBio Glycan Map (2.1 x 100mm, 2.7µm) |
MS Type | ESI |
MS instrument type | QTOF |
MS instrument name | Agilent 6540 QTOF |
Ion Mode | NEGATIVE |
Units | arbitrary units |
Chromatography:
Chromatography ID: | CH002062 |
Instrument Name: | Agilent 6545 QTOF-MS |
Column Name: | AdvanceBio Glycan Map (2.1 x 100mm, 2.7µm) |
Column Temperature: | 35 |
Flow Gradient: | 100% B, 0.5 min; 95% B, 2.0 min; 60% B, 3.0 min; 35% B, 5 min; hold 0.25 min; 0% B, 6 min; hold 0.5 min; 100% B, 7.8 min; equilibrate for 1.7 min. |
Flow Rate: | 0.2 mL/min |
Solvent A: | 88% water/12% acetonitrile; 10 mM ammonium acetate; titrated with formic acid and ammonium hydroxide to pH 6.85 |
Solvent B: | 90% acetonitrile/10% water; 10 mM ammonium acetate; titrated with formic acid and ammonium hydroxide to pH 6.85 |
Chromatography Type: | HILIC |
MS:
MS ID: | MS002583 |
Analysis ID: | AN002787 |
Instrument Name: | Agilent 6540 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
MS Comments: | LC/MS analysis was conducted with the Agilent 6545 QTOF-MS combined with 1290 Infinity II UHPLC system (Agilent Technologies, Wilmington, DE, USA). Only LC/MS grade solvents and additives purchased from Covachem (CovaChem, LLC., Loves Park, IL, USA) were used to prepare mobile phases and wash solutions. Wash cycles consisting of strong wash (50% Methanol, 25% Isopropanol, and 25% Water), weak wash (90% Acetonitrile and 10 % Water), and seal wash (10% Isopropanol and 90% water) were implemented to eliminate carryover between injections. Dried extracts were reconstituted in 80 µL 60:40 MeOH/H2O and samples were injected (8 µL) to resolve analytes using Infinity 1290 in-line filter combined with AdvanceBio Glycan Map 2.1 x 100mm, 2.7µm column (Agilent Technologies, Wilmington, DE., USA) set at 35 0C. The solvent buffers were composed of mobile phase A (10 mM ammonium acetate in 88% water/ 12% acetonitrile) and mobile phase B (10 mM ammonium acetate in 90 % Acetonitrile) titrated with formic acid and ammonium hydroxide to pH 6.85. The linear gradient was executed at flow rate 0.2 mL/min, as follows: 100 % B, 0.5 min; 95% B, 2.0 min; 60 % B, 3.0 min; 35 % B, 5 min; hold 0.25 min; 0% B, 6 min; hold 0.5 min; 100 % B, 7.8 min; equilibrate for 1.7 min. The mass analyzer acquisition parameters include drying gas temperature, 250 0C; drying gas flow, 9 L/min; sheath gas temperature, 325 0C; sheath gas flow, 11 L/min; nebulizer, 45 psig. Mass spectra were acquired at 3.0 spectra/s in negative electrospray ionization (ESI-) mode for a mass range from 72 to 1200 m/z using a voltage gradient of capillary 3000 V, nozzle 2000 V, fragmentor 80 V, skimmer 50 V, and octopole radio frequency 750 V. |
Ion Mode: | NEGATIVE |