Summary of Study ST001916

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001208. The data can be accessed directly via it's Project DOI: 10.21228/M8JX2X This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST001916
Study Title	Myocardial Rev-erb-mediated diurnal metabolic rhythm (Part 2/3)
Study Summary	Agonists and antagonists of nuclear receptor Rev-erbα/β, key components of the circadian clock, can benefit the heart. Here, we show that mice with cardiomyocyte-specific knockout (KO) of Rev-erbα/β display progressive cardiac dilation and lethal heart failure. Inducible ablation of Rev-erbα/β in adult hearts causes similar phenotypes. Impaired fatty acid oxidation in the KO myocardium, particularly in the light cycle, precedes contractile dysfunctions with a reciprocal overreliance on carbohydrate utilization, particularly in the dark cycle. These findings delineate temporal coordination between clock-mediated anticipation and nutrient-induced response in myocardial metabolism.
Institute	Baylor College of Medicine
Last Name	Song
First Name	Shiyang
Address	One Baylor Plaza,Houston, TX, 77030
Email	shiyangs@bcm.edu
Phone	7137983159
Submit Date	2021-09-10
Raw Data Available	Yes
Analysis Type Detail	LC-MS
Release Date	2022-12-24
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001208
Project DOI:	doi: 10.21228/M8JX2X
Project Title:	Myocardial Rev-erb-mediated diurnal metabolic rhythm
Project Summary:	Agonists and antagonists of nuclear receptor Rev-erbα/β, key components of the circadian clock, can benefit the heart. Here, we show that mice with cardiomyocyte-specific knockout (KO) of Rev-erbα/β display progressive cardiac dilation and lethal heart failure. Inducible ablation of Rev-erbα/β in adult hearts causes similar phenotypes. Impaired fatty acid oxidation in the KO myocardium, particularly in the light cycle, precedes contractile dysfunctions with a reciprocal overreliance on carbohydrate utilization, particularly in the dark cycle. These findings delineate temporal coordination between clock-mediated anticipation and nutrient-induced response in myocardial metabolism.
Institute:	Baylor College of Medicine
Last Name:	Song
First Name:	Shiyang
Address:	One Baylor Plaza, Houston, Texas, 77030, USA
Email:	shiyangs@bcm.edu
Phone:	7137983159

Subject:

Subject ID:	SU001994
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Group	Genotype	Experimental variables
SA177718	KO_CD_3	KO_CD	Rev-erb cardiomyocyte specific knock out	heart ventrcle harvest from KO mouse fed with chow diet
SA177719	KO_CD_2	KO_CD	Rev-erb cardiomyocyte specific knock out	heart ventrcle harvest from KO mouse fed with chow diet
SA177720	KO_CD_1	KO_CD	Rev-erb cardiomyocyte specific knock out	heart ventrcle harvest from KO mouse fed with chow diet
SA177715	KO-HFHSD_2	KO-HFHSD	Rev-erb cardiomyocyte specific knock out	heart ventrcle harvest from KOmouse fed with high fat high sucrose diet
SA177716	KO-HFHSD_3	KO-HFHSD	Rev-erb cardiomyocyte specific knock out	heart ventrcle harvest from KOmouse fed with high fat high sucrose diet
SA177717	KO-HFHSD_1	KO-HFHSD	Rev-erb cardiomyocyte specific knock out	heart ventrcle harvest from KOmouse fed with high fat high sucrose diet
SA177721	WT_CD_2	WT_CD	wild type control	heart ventrcle harvest from WT mouse fed with chow diet
SA177722	WT_CD_3	WT_CD	wild type control	heart ventrcle harvest from WT mouse fed with chow diet
SA177723	WT_CD_1	WT_CD	wild type control	heart ventrcle harvest from WT mouse fed with chow diet
SA177724	WT_HFHSD_1	WT_HFHSD	wild type control	heart ventrcle harvest from WT mouse fed with high fat high sucrose diet
SA177725	WT_HFHSD_2	WT_HFHSD	wild type control	heart ventrcle harvest from WT mouse fed with high fat high sucrose diet
SA177726	WT_HFHSD_3	WT_HFHSD	wild type control	heart ventrcle harvest from WT mouse fed with high fat high sucrose diet

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO001987
Collection Summary:	Snap-frozen heart ventricles were collected from both WT and Rev-erb cardiomyocyte-specific KO mice fed with either chow diet or high fat high sucrose diet(HFHSD), HFHSD start at 8 weeks old and mice were harvest at 4.5 months of age.
Sample Type:	Heart

Treatment:

Treatment ID:	TR002006
Treatment Summary:	mice were fed with either the chow diet or high-fat high sucrose diet as indicated.

Sample Preparation:

Sampleprep ID:	SP002000
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.

Sampleprep ID:

SP002000

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	AN003114
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	Triple quadrupole
MS instrument name	Agilent 6490 QQQ
Ion Mode	POSITIVE
Units	pmoles/l

Chromatography:

Chromatography ID:	CH002299
Chromatography 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.
Instrument Name:	Agilent 1290
Column Name:	Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
Chromatography Type:	GC

MS:

MS ID:	MS002895
Analysis ID:	AN003114
Instrument Name:	Agilent 6490 QQQ
Instrument Type:	Triple quadrupole
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