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MB Sample ID: SA323398
Local Sample ID: | SHMT2flox_KO_35_liver |
Subject ID: | SU003093 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU003093 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
SHMT2flox_KO_35_liver | SA323398 | FL038638 | Liver | Sample type |
SHMT2flox_KO_35_liver | SA323398 | FL038638 | Liver KO | Genotype |
SHMT2flox_KO_35_liver | SA323398 | FL038638 | None | Treatment |
Collection:
Collection ID: | CO003086 |
Collection Summary: | For pharmacological inhibition of SHMT, mice were treated with Vehicle or SHIN2 for 12 hours and then blood serum and liver samples were collected. For genetic loss of Shmt2, blood serum and liver samples were collected from mice 21 days after liver-specific gene knockout. |
Sample Type: | Blood (serum) and Liver |
Treatment:
Treatment ID: | TR003102 |
Treatment Summary: | For pharmacological inhibition of SHMT, mice (C57BL/6N) were divided into two groups and received Vehicle (20% 2-hydroxypropyl-β-cyclodextrin) or SHIN2 (200 mg/kg) for 12 hours. For genetic loss of Shmt2, Shmt2(flox/flox) mice and wild-type litter mate controls were injected with AAV8-TBG-Cre viral particles to induce liver-specific gene knockout and samples were harvested 21 days later. |
Sample Preparation:
Sampleprep ID: | SP003099 |
Sampleprep Summary: | Water soluble metabolites were extracted from serum and liver samples. 3ul of serum was extracted with 120 ul (40X) of 100% methanol, cooled on ice for 10 minutes, centrifuged at 16,000 x g for 30 minutes, and supernatant collected. 20mg of ground liver tissue was extracted with 800ul of 40:40:20 methanol:acetonitrile:water, cooled on ice for 10 minutes, centrifuged at 16,000 x g for 30 minutes, and supernatant collected. |
Combined analysis:
Analysis ID | AN004897 | AN004898 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | HILIC | HILIC |
Chromatography system | Thermo Vanquish | Thermo Vanquish |
Column | Waters XBridge BEH Amide (100 x 2.1mm,2.5um) | Waters XBridge BEH Amide (100 x 2.1mm,2.5um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
Ion Mode | NEGATIVE | POSITIVE |
Units | Peak area | Peak area |
Chromatography:
Chromatography ID: | CH003695 |
Instrument Name: | Thermo Vanquish |
Column Name: | Waters XBridge BEH Amide (100 x 2.1mm,2.5um) |
Column Temperature: | 25°C |
Flow Gradient: | 0 minutes, 85% B; 2 minutes, 85% B; 3 minutes, 80% B; 5 minutes, 80% B; 6 minutes, 75% B; 7 minutes, 75% B; 8 minutes, 70% B; 9 minutes, 70% B; 10 minutes, 50% B; 12 minutes, 50% B; 13 minutes, 25% B; 16 minutes, 25% B; 18 minutes, 0% B; 23 minutes, 0% B; 24 minutes, 85% B; 30 minutes, 85% B |
Flow Rate: | 150 μl/min |
Solvent A: | 95% water/5% acetonitrile with 20 mM ammonium acetate, 20 mM ammonium hydroxide, pH 9.4 |
Solvent B: | 100% acetonitrile |
Chromatography Type: | HILIC |
MS:
MS ID: | MS004641 |
Analysis ID: | AN004897 |
Instrument Name: | Thermo Q Exactive Plus Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | MS full scans were in negative ion mode with a resolution of 140,000 at m/z 200 and scan range of 70–1,000 m/z. The automatic gain control (AGC) target was 1 × 10^6. LC-MS peak files were analyzed and visualized with El-MAVEN (Elucidata) using 5 ppm ion extraction window, minimum peak intensity of 1 x 10^5 ions, and minimum signal to background blank ratio of 2. |
Ion Mode: | NEGATIVE |
MS ID: | MS004642 |
Analysis ID: | AN004898 |
Instrument Name: | Thermo Q Exactive Plus Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | MS full scans were in positive ion mode with a resolution of 140,000 at m/z 200 and scan range of 70–1,000 m/z. The automatic gain control (AGC) target was 1 × 10^6. LC-MS peak files were analyzed and visualized with El-MAVEN (Elucidata) using 5 ppm ion extraction window, minimum peak intensity of 1 x 10^5 ions, and minimum signal to background blank ratio of 2. |
Ion Mode: | POSITIVE |