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MB Sample ID: SA093739
Local Sample ID: | SG228 |
Subject ID: | SU001362 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | SmoA1-Math-GFP |
Age Or Age Range: | 12-36 weeks |
Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001362 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | SmoA1-Math-GFP |
Age Or Age Range: | 12-36 weeks |
Gender: | Male and female |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
SG228 | SA093739 | FL013416 | SmoA1-Math-GFP | Mice strain |
SG228 | SA093739 | FL013416 | PTMT | Group |
Collection:
Collection ID: | CO001356 |
Collection Summary: | Mice brain and spinal cord were dissected from each mouse and fluorescence microscopy was used to visualize the tumors. Mice having a GFP signal in the cerebellum only were designated as having a primary tumor without metastasis (PT group, n=18). Mice having a strong GFP signal in the cerebellum and positive GFP signal in the spinal cord were designated as having a primary tumor with metastasis (PTMT group, n=7). With aid of GFP visualization, the primary tumor in each mouse brain was cut from the cerebellum, and immediately frozen using liquid nitrogen, and stored at -80 °C. |
Sample Type: | Brain |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR001377 |
Treatment Summary: | SmoA1-Math1-GFP mice were generated by crossing SmoA1 mice with Math1-driven GFP reporter mice. All mice were kept under the same condition and typically developed detectable MB tumors by MR imaging and clinical symptoms around 23 weeks. |
Sample Preparation:
Sampleprep ID: | SP001370 |
Sampleprep Summary: | Frozen mice brain tissue samples were cryo-pulverized with liquid nitrogen and weighed. 2-propanol (20 uL/mg) was added to the cryo-pulverized tissue samples to precipitate proteins. Samples were vortex-mixed for 1 min, and centrifuged at 13,000 rpm for 7 min. Following centrifugation, 100 uL of supernatant was transferred to an autosampler vial and analyzed with UPLC-MS. A blank sample, prepared with 100 uL 2-propanol, underwent the same process as the murine tumor samples. A pooled quality control (QC) sample was prepared by mixing a 10 uL aliquot of supernatant of each sample. |
Combined analysis:
Analysis ID | AN002143 | AN002144 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
Column | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
Ion Mode | POSITIVE | NEGATIVE |
Units | Normalized Peak Abundance | Normalized Peak Abundance |
Chromatography:
Chromatography ID: | CH001569 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
Column Temperature: | 55 |
Sample Injection: | 5μL |
Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate |
Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS001995 |
Analysis ID: | AN002143 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Samples were analyzed in positive and negative ion modes for RP chromatography. Spectral features were extracted from the raw data using Progenesis QI v2.1 software. |
Ion Mode: | POSITIVE |
Capillary Temperature: | 275 °C |
Spray Voltage: | 3.0 kV |
MS ID: | MS001996 |
Analysis ID: | AN002144 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Samples were analyzed in positive and negative ion modes for RP chromatography. Spectral features were extracted from the raw data using Progenesis QI v2.1 software. |
Ion Mode: | NEGATIVE |
Capillary Temperature: | 275 °C |
Spray Voltage: | -2.8 kV |