Return to study ST002123 main page

MB Sample ID: SA204271

Local Sample ID:WT_1
Subject ID:SU002208
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Select appropriate tab below to view additional metadata details:


Subject:

Subject ID:SU002208
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
WT_1SA204271FL025059Wild-typeGenotype
WT_1SA204271FL0250595 FU 2 weeksTreatment
WT_1SA204271FL0250591fBatch
WT_1SA204271FL025059Lin– Scal1+ c-Kit+ (LSK)Source_Name[gating]

Collection:

Collection ID:CO002201
Collection Summary:2 million HSPCs (LSK cells) were sorted stored at -80 ℃.
Sample Type:Bone marrow

Treatment:

Treatment ID:TR002220
Treatment Summary:Wild-type and GCN2 knockout mice were intraperitoneally injected with 10 mg/kg 5FU (F6627-5G, Sigma-Aldrich) for 14 days. HSPCs were stained and sorted from treated mice.

Sample Preparation:

Sampleprep ID:SP002214
Sampleprep Summary:The cell samples were extracted with 800 µL of 80% methanol and vortexed for 1 min. Then, ultrasonicate for 30 min at 4℃ were performed, letting stand in -40℃ refrigerator for 1 h. After that, the samples were vortexed for 30s and set at 4℃ for 30 min. The samples were centrifuged at 12,000 rpm, 4℃ for 15 min. Taking all the supernatant in the centrifuge tube and concentrating to remove the organic reagents and water. 100 µL of 80% methanol would be used to reconstitute, vortex again for 1 min. The supernatant was transferred by centrifugation to the sample vial for liquid chromatography-mass spectrometry (LC-MS) analysis.

Combined analysis:

Analysis ID AN003476
Analysis type MS
Chromatography type HILIC
Chromatography system ACQUITY UPLC
Column Waters ACQUITY UPLC BEH Amide
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode UNSPECIFIED
Units AU

Chromatography:

Chromatography ID:CH002565
Instrument Name:ACQUITY UPLC
Column Name:Waters ACQUITY UPLC BEH Amide
Column Temperature:40
Flow Gradient:The gradient program started at 85% (B) and was reduced to 70% (B) over 9 min, then reduced from 70% (B) to 30% (B) over 3 min, followed by wash with 30% (B) for another 3 min, and finally 5 min re-equilibration with 85% (B).
Flow Rate:0.35ml/min
Solvent A:100% water; 10mM ammonium formate
Solvent B:100% acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS003237
Analysis ID:AN003476
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:LC-MS data was acquired on SCIEX 5500 QQQ mass spectrometer (Applied Biosystems, Foster City, CA, USA) coupled with high-performance liquid chromatography (HPLC) system ACQUITY UPLC (Waters, Milford, MA, USA). Chromatographic separation was performed on a ACQUITY UPLC BEH Amide Column (1.7 µm, 2.1 mm x 100 mm, Waters, Milford, MA, USA). The mobile phase (A) was 10 mM ammonium formate and (B) acetonitrile. The gradient program started at 85% (B) and was reduced to 70% (B) over 9 min, then reduced from 70% (B) to 30% (B) over 3 min, followed by wash with 30% (B) for another 3 min, and finally 5 min re-equilibration with 85% (B). The flow rate was 0.35 mL/min and column compartment temperature was 40ºC. The total run time was 20 min with an injection sample volume of 5 µL.
Ion Mode:UNSPECIFIED
  logo