Return to study ST003436 main page

MB Sample ID: SA378176

Local Sample ID:61 F09 Blue
Subject ID:SU003563
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:NOD Scid Gamma (NSG)
Age Or Age Range:3 months
Weight Or Weight Range:24-33 g
Gender:Female
Animal Animal Supplier:Wistar Animal Facility
Animal Housing:Wistar Animal Facility
Animal Feed:Standard chow diet
Species Group:Mammals

Select appropriate tab below to view additional metadata details:

Subject:

Subject ID:SU003563
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:NOD Scid Gamma (NSG)
Age Or Age Range:3 months
Weight Or Weight Range:24-33 g
Gender:Female
Animal Animal Supplier:Wistar Animal Facility
Animal Housing:Wistar Animal Facility
Animal Feed:Standard chow diet
Species Group:Mammals

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
61 F09 BlueSA378176FL043640FBS-based standardSample source
61 F09 BlueSA378176FL043640FBS-based standardSample Type
61 F09 BlueSA378176FL043640NADrug Treatment
61 F09 BlueSA378176FL043640NATime post-injection

Collection:

Collection ID:CO003556
Collection Summary:Plasma metabolomics samples were prepared from whole blood mixed with EDTA to 10 mM final concentration. To separate plasma, blood samples were centrifuged at 2,000 g and 4 °C for 10 min. Then, 50 µl of plasma were mixed with 450 µl of 100% methanol to reach 90% final methanol concentration. Tissue metabolite extracts were prepared from ~50 mg snap-frozen tissue samples. Each sample was weighed while frozen. Frozen samples were ground at the temperature of liquid nitrogen by Retch Cryomill. Then, 80% methanol was added to each tube at a ratio of 1 ml per 50 mg of tissue. Regardless of the type of metabolite extracts, all samples were centrifuged at 18,000 g and 4 °C for 20 min. The supernatant was then transferred to new Eppendorf tubes and centrifuged again with the same parameters. After centrifugation, the extracts were transferred to glass LC-MS vials.
Collection Protocol Filename:DM_metabolomics_samples.txt
Sample Type:Brain, Heart, Liver, Blood(plasma)
Collection Method:80% methanol extraction for organs, 90% for plasma
Storage Conditions:-80℃
Collection Vials:1.5 ml plastic centrifuge tubes
Storage Vials:1.5 ml plastic centrifuge tubes

Treatment:

Treatment ID:TR003572
Treatment Summary:Cells were grown in RPMI-1640 supplemented with 10% dialyzed FBS and treated with various concentrations of dimethylmalonate (DMM) for 24 h.
Treatment Compound:Fasnall (1-benzyl-N-{5,6-dimethylthieno[2,3-d]pyrimidin-4-yl}pyrrolidin-3-amine, Enamine EN300-14327544)
Treatment Vehicle:1:1 DMSO:PBS

Sample Preparation:

Sampleprep ID:SP003570
Sampleprep Summary:Plasma metabolomics samples were prepared from whole blood mixed with EDTA to 10 mM final concentration. To separate plasma, blood samples were centrifuged at 2,000 g and 4 °C for 10 min. Then, 50 µl of plasma were mixed with 450 µl of 100% methanol to reach 90% final methanol concentration. Tissue metabolite extracts were prepared from ~50 mg snap-frozen tissue samples. Each sample was weighed while frozen. Frozen samples were ground at the temperature of liquid nitrogen by Retch Cryomill. Then, 80% methanol was added to each tube at a ratio of 1 ml per 50 mg of tissue. Regardless of the type of metabolite extracts, all samples were centrifuged at 18,000 g and 4 °C for 20 min. The supernatant was then transferred to new Eppendorf tubes and centrifuged again with the same parameters. After centrifugation, the extracts were transferred to glass LC-MS vials.
Sampleprep Protocol Filename:DM_metabolomics_samples.txt
Processing Storage Conditions:4℃
Extraction Method:80% methanol for organs, 90% for plasma
Extract Enrichment:None
Extract Cleanup:None
Extract Storage:-80℃
Sample Resuspension:None
Sample Derivatization:None
Sample Spiking:None
Subcellular Location:Intracellular metabolites and medium metabolites

Combined analysis:

Analysis ID AN005645 AN005646
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Shimadzu 20AD Shimadzu 20AD
Column Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap ABI Sciex 5500 QTrap
Ion Mode NEGATIVE POSITIVE
Units Counts per second (cps) Counts per second (cps)

Chromatography:

Chromatography ID:CH004285
Instrument Name:Shimadzu 20AD
Column Name:Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Column Pressure:900-3000 psi
Column Temperature:40
Flow Gradient:0-12.5 min, 80-30% B; 12.5-15 min, 30% B; 15-15.2 min, 30-80% B; 15.2-22.5 min, 80% B
Flow Rate:0-20 min, 0.2 ml/min; 20-21 min 0.2-0.3 ml/min; 21-22 min, 0.3 ml/min; 22-22.1 min, 0.2 ml/min; 22.1-22.5 min, 0.2 ml/min
Injection Temperature:4
Sample Injection:1-5 ul
Solvent A:100% Water; 0.01% ammonium hydroxide; 20 mM ammonium bicarbonate
Solvent B:100% Acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS005369
Analysis ID:AN005645
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Data were analyzed with SCIEX Multiquant 3.0.3.
Ion Mode:NEGATIVE
Capillary Temperature:500 °C
Capillary Voltage:-4500
Dry Gas Flow:70
Dry Gas Temp:500 °C
Ion Source Temperature:500 °C
Ion Spray Voltage:-4500
Mass Accuracy:UNIT
Source Temperature:500 °C
Spray Voltage:-4500
Desolvation Gas Flow:70
Desolvation Temperature:500 °C
  
MS ID:MS005370
Analysis ID:AN005646
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Data were analyzed with SCIEX Multiquant 3.0.3.
Ion Mode:POSITIVE
Capillary Temperature:500 °C
Capillary Voltage:4500
Dry Gas Flow:70
Dry Gas Temp:500 °C
Ion Source Temperature:500 °C
Ion Spray Voltage:4500
Mass Accuracy:UNIT
Source Temperature:500 °C
Spray Voltage:4500
Desolvation Gas Flow:70
Desolvation Temperature:500 °C
  logo