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MB Sample ID: SA177728
Local Sample ID: | KO_ZT18_1 |
Subject ID: | SU001995 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Age Or Age Range: | 10 weeks |
Gender: | Male |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001995 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Age Or Age Range: | 10 weeks |
Gender: | Male |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
KO_ZT18_1 | SA177728 | FL021975 | KO_ZT18 | Group |
KO_ZT18_1 | SA177728 | FL021975 | Rev-erb cardiomyocyte specific knock out | Genotype |
KO_ZT18_1 | SA177728 | FL021975 | KO mouse heart ventrcle harvest at ZT18 | Experimental variables |
Collection:
Collection ID: | CO001988 |
Collection Summary: | Snap-frozen heart ventricles were collected from both WT and Rev-erb cardiomyocyte-specific KO mice at ZT6 or ZT18 |
Sample Type: | Heart |
Treatment:
Treatment ID: | TR002007 |
Treatment Summary: | No special treatment |
Sample Preparation:
Sampleprep ID: | SP002001 |
Sampleprep Summary: | Heart ventricle tissues were harvested from male mice at 2.5 months of age (n = 3 at each condition) and snap-frozen in liquid nitrogen. Data were acquired in multiple reaction monitoring (MRM) using Agilent QQQ LC-MS systems. Separation of TCA and glycolysis metabolites were performed using 5 mM ammonium acetate in water as buffer pH 9.9 (A), and 100% acetonitrile as buffer (B) using Luna 3 µM NH2 column (Phenomenex, Torrance, CA) and measured 6495 triple quadrupole mass spectrometer via ESI negative mode (Agilent Technologies, Santa Clara, CA). The Gradient used is as follows: 0-20 min-80% B (Flow rate 0.2ml/min); 20-20.10 min- 80% to 2 % B; 20.10-25 min-2% B (Flow rate 0.3ml/min); 25-30 min 80% B (Flowrate 0.35ml/min); 30-35 min-80%B (Flow rate 0.4ml/min); 35-38 min 80% B (Flow rate 0.4ml/min); followed by re-equilibration at the end of the gradient to the initial starting condition 80% B at Flow rate of 0.2 ml/min. Separation and measurement of amino acids were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B, 13 min 2% of B followed by re-equilibration at the end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of CoA's and carnitines were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. Gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B,13 min 2% of B followed by re-equilibration at end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of nucleotides were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0-6 min 2% B, 6-6.50 min 30% B, 7-12 min 95% B, 12-13 min 2% B, and re-equilibration till the end of the gradient 20 min. Flow rate: 0.2 ml/min). The data were normalized with internal standards, and log2 transformed on a per-sample, per-method basis. Statistical analyses were performed with either ANOVA or t-test in R Studio (R Studio Inc., Boston, MA). Differential metabolites were identified by adjusting the p-values for multiple testing at an FDR (Benjamini Hochberg method) threshold of <0.25. |
Combined analysis:
Analysis ID | AN003115 |
---|---|
Analysis type | MS |
Chromatography type | GC |
Chromatography system | Agilent 1290 |
Column | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
MS Type | ESI |
MS instrument type | Other |
MS instrument name | Agilent 6490 QQQ |
Ion Mode | POSITIVE |
Units | pmoles/l |
Chromatography:
Chromatography ID: | CH002300 |
Chromatography Summary: | Separation of TCA and glycolysis metabolites were performed using 5 mM ammonium acetate in water as buffer pH 9.9 (A), and 100% acetonitrile as buffer (B) using Luna 3 µM NH2 column (Phenomenex, Torrance, CA) and measured 6495 triple quadrupole mass spectrometer via ESI negative mode (Agilent Technologies, Santa Clara, CA). The Gradient used is as follows: 0-20 min-80% B (Flow rate 0.2ml/min); 20-20.10 min- 80% to 2 % B; 20.10-25 min-2% B (Flow rate 0.3ml/min); 25-30 min 80% B (Flowrate 0.35ml/min); 30-35 min-80%B (Flow rate 0.4ml/min); 35-38 min 80% B (Flow rate 0.4ml/min); followed by re-equilibration at the end of the gradient to the initial starting condition 80% B at Flow rate of 0.2 ml/min. Separation and measurement of amino acids were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B, 13 min 2% of B followed by re-equilibration at the end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of CoA's and carnitines were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. Gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B,13 min 2% of B followed by re-equilibration at end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of nucleotides were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0-6 min 2% B, 6-6.50 min 30% B, 7-12 min 95% B, 12-13 min 2% B, and re-equilibration till the end of the gradient 20 min. Flow rate: 0.2 ml/min). |
Instrument Name: | Agilent 1290 |
Column Name: | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
Chromatography Type: | GC |
MS:
MS ID: | MS002896 |
Analysis ID: | AN003115 |
Instrument Name: | Agilent 6490 QQQ |
Instrument Type: | Other |
MS Type: | ESI |
MS Comments: | The data were normalized with internal standards, and log2 transformed on a per-sample, per-method basis. Statistical analyses were performed with either ANOVA or t-test in R Studio (R Studio Inc., Boston, MA). Differential metabolites were identified by adjusting the p-values for multiple testing at an FDR (Benjamini Hochberg method) threshold of <0.25. |
Ion Mode: | POSITIVE |