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MB Sample ID: SA323406

Local Sample ID:SHMT2flox_WT_37_liver
Subject ID:SU003093
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

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Subject:

Subject ID:SU003093
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
SHMT2flox_WT_37_liverSA323406FL038639LiverSample type
SHMT2flox_WT_37_liverSA323406FL038639Wild-typeGenotype
SHMT2flox_WT_37_liverSA323406FL038639NoneTreatment

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
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