Return to study ST002706 main page
MB Sample ID: SA272179
Local Sample ID: | PL6 |
Subject ID: | SU002811 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | B6.129-Arntltm1Bra/J |
Age Or Age Range: | 40 weeks |
Gender: | Male |
Animal Feed: | Ad libitum |
Animal Water: | Ad libitum |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002811 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | B6.129-Arntltm1Bra/J |
Age Or Age Range: | 40 weeks |
Gender: | Male |
Animal Feed: | Ad libitum |
Animal Water: | Ad libitum |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
PL6 | SA272179 | FL035256 | Bmal1-KO | Genotype |
PL6 | SA272179 | FL035256 | Control | Treatment |
Collection:
Collection ID: | CO002804 |
Collection Summary: | Mice were anesthetized using isofluorane. Blood was collected by intracardiac puncture. EDTA was used as anticoagulant. Blood was centrifuged at 2,000xg for 15 mins and plasma was collected and subsequently frozen in liquid nitrogen. Samples are stored at -80°C. |
Sample Type: | Blood (plasma) |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR002820 |
Treatment Summary: | Bmal1-KO+AAV mice were systemically infected in the subxiphoid region with 20μl containing 2 × 10^11 genome copies of AAV9 on postnatal day 5. |
Sample Preparation:
Sampleprep ID: | SP002817 |
Sampleprep Summary: | All provided samples were extracted following our cellular extraction procedure with pre-normalization to the sample protein content. Each extract was spiked with 1 ul of standard mixture consisting of deuterium labeled carnitine, acetylcarnitine, propionylcarnitine, butyrylcarnitine, isovalerylcarnitine, octanoylcarnitine, myristoylcarnitine and palmitoylcarnitine to targeted identification of carnitines in the sample. Metabolite extraction was done by protein precipitation using 200 µl of 8:1:1 Acetonitrile: Methanol: Acetone with 0.1% formic acid. Further protein precipitation was allowed by incubating the samples at 4°C for 20 min. Samples were placed in an ultrasonic bath for 10 min and then centrifuged at 20 000 xg for 5min at 4°C to pellet the protein. 190 µl supernatant was transferred from each sample into clean tube and dried under a gentle stream of nitrogen at 30°C. The dried extracts were re-suspended with 25 µL water with 0.1% formic acid. Resuspension was allowed at 4°C for 10 -15 min then samples were centrifuged at 20000 xg for 5 min at 4°C. Supernatants were transferred into clean LC-vials for targeted LC-MS quantitation on a Thermo Q-Exactive Oribtrap mass spectrometer with Dionex UHPLC and autosampler. |
Combined analysis:
Analysis ID | AN004387 | AN004388 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Thermo Dionex | Thermo Dionex |
Column | ACE Excel 2 C18-PFP (100 x 2.1mm,2um) | ACE Excel 2 C18-PFP (100 x 2.1mm,2um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE | NEGATIVE |
Units | Peak height | Peak height |
Chromatography:
Chromatography ID: | CH003291 |
Chromatography Summary: | Global metabolomics profiling was performed on a Thermo Q-Exactive Oribtrap mass spectrometer with Dionex UHPLC and autosampler. Each extract was spiked with 1 ul of standard mixture consisting of deuterium labeled carnitine, acetylcarnitine, propionylcarnitine, butyrylcarnitine, isovalerylcarnitine, octanoylcarnitine, myristoylcarnitine and palmitoylcarnitine to targeted identification of carnitines in the sample. All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 2 Excel-C18 pfp, 100x2.1mm, 2um column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions. |
Instrument Name: | Thermo Dionex |
Column Name: | ACE Excel 2 C18-PFP (100 x 2.1mm,2um) |
Column Temperature: | 25°C |
Flow Gradient: | - |
Flow Rate: | 350 µL/min |
Solvent A: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile |
Chromatography Type: | Reversed phase |
Solvent C: | - |
MS:
MS ID: | MS004136 |
Analysis ID: | AN004387 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 18-pfp 100 x 2.1 mm, 2 µm column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions. |
Ion Mode: | POSITIVE |
MS ID: | MS004137 |
Analysis ID: | AN004388 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 18-pfp 100 x 2.1 mm, 2 µm column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions. |
Ion Mode: | NEGATIVE |