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MB Sample ID: SA247366
| Local Sample ID: | Zha-Jas-20210625-04 |
| Subject ID: | SU002557 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002557 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Zha-Jas-20210625-04 | SA247366 | FL031105 | IR + LNP | Treatment |
Collection:
| Collection ID: | CO002550 |
| Collection Summary: | Magnetic bead isolation of cells To isolate specific populations of cells, single-cell suspensions as isolated above are preblocked with anti-CD16/32 for 15 min at 4°C. We then used the biotinylated anti-Gr1 (clone RB6-8C5) (all from Thermo Fisher Scientific) to label murine myeloid cells. Next, the cells were washed and then incubated with anti-biotin magnetic beads (Miltenyi Biotec) before performing manual positive selection using MS columns (Miltenyi Biotec). Purified cells were analyzed for all downstream metabolic analyses. |
| Sample Type: | Brain |
Treatment:
| Treatment ID: | TR002569 |
| Treatment Summary: | GR1 cells were isolated from mice after 9Gy Radiation or 9Gy radiation and nanoparticle therapy |
Sample Preparation:
| Sampleprep ID: | SP002563 |
| Sampleprep Summary: | Isolated TAMC and CD8+ T cells samples were dried using a SpeedVac. Acetonitrile (50%) was added to the tube for reconstitution following overtaxing for 30 s. Sample solution was then centrifuged for 15 min at 20,000g and 4°C. Supernatant was collected for LC-MS analysis. The mobile phase A contained 95% water/5% acetonitrile (v/v), 20 mM ammonium hydroxide, and 20 mM ammonium acetate (pH 9.0); phase B was 100% acetonitrile. The gradient was performed as follows: 0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1 to 18 min, 75% A; and 18 to 25 min, 15% A with a flow rate of 400 μl/min. The capillary of the electrospray ionization source was set to 275°C, with sheath gas at 45 arbitrary units, auxiliary gas at 5 arbitrary units, and the spray voltage at 4.0 kV. In positive/negative polarity switching mode, a mass/charge ratio (m/z) scan range from 70 to 850 was chosen and MS1 data were collected at a resolution of 70,000. The automatic gain control target was set at 1 × 106, and the maximum injection time was 200 ms. The top five precursor ions were subsequently fragmented, in a data-dependent manner, using the higher-energy collisional dissociation cell set to 30% normalized collision energy in MS2 at a resolution power of 17,500. |
Combined analysis:
| Analysis ID | AN004023 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Q Exactive™ Plus Hybrid Quadrupole-Orbitrap™ Mass Spectrometer |
| Column | Water's Xbridge amide (100 x 3mm, 3.5 um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | Normalized peak area |
Chromatography:
| Chromatography ID: | CH002973 |
| Chromatography Summary: | Samples were analyzed by high-performance LC (HPLC) and high-resolution MS and MS/MS (HPLC-MS/MS). The system consists of Thermo Q Exactive with an electrospray source and an UltiMate3000 (Thermo Fisher Scientific) series HPLC consisting of a binary pump, degasser, and autosampler outfitted with an XBridge Amide column (Waters; dimensions of 4.6 mm by 100 mm and a 3.5-μm particle size). |
| Instrument Name: | Q Exactive™ Plus Hybrid Quadrupole-Orbitrap™ Mass Spectrometer |
| Column Name: | Water's Xbridge amide (100 x 3mm, 3.5 um) |
| Column Temperature: | 275 |
| Flow Gradient: | 0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1 to 18 min, 75% A; and 18 to 25 min, 15% A |
| Flow Rate: | 400 μl/min |
| Solvent A: | 95% water/5% acetonitrile; 20 mM ammonium hydroxide; 20 mM ammonium acetate (pH 9.0) |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003770 |
| Analysis ID: | AN004023 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Isolated TAMC and CD8+ T cells samples were dried using a SpeedVac. Acetonitrile (50%) was added to the tube for reconstitution following overtaxing for 30 s. Sample solution was then centrifuged for 15 min at 20,000g and 4°C. Supernatant was collected for LC-MS analysis. The mobile phase A contained 95% water/5% acetonitrile (v/v), 20 mM ammonium hydroxide, and 20 mM ammonium acetate (pH 9.0); phase B was 100% acetonitrile. The gradient was performed as follows: 0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1 to 18 min, 75% A; and 18 to 25 min, 15% A with a flow rate of 400 μl/min. The capillary of the electrospray ionization source was set to 275°C, with sheath gas at 45 arbitrary units, auxiliary gas at 5 arbitrary units, and the spray voltage at 4.0 kV. In positive/negative polarity switching mode, a mass/charge ratio (m/z) scan range from 70 to 850 was chosen and MS1 data were collected at a resolution of 70,000. The automatic gain control target was set at 1 × 106, and the maximum injection time was 200 ms. The top five precursor ions were subsequently fragmented, in a data-dependent manner, using the higher-energy collisional dissociation cell set to 30% normalized collision energy in MS2 at a resolution power of 17,500. |
| Ion Mode: | UNSPECIFIED |
