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.

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Study IDST001916
Study TitleMyocardial Rev-erb-mediated diurnal metabolic rhythm (Part 2/3)
Study SummaryAgonists 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 NameSong
First NameShiyang
AddressOne Baylor Plaza,Houston, TX, 77030
Emailshiyangs@bcm.edu
Phone7137983159
Submit Date2021-09-10
Raw Data AvailableYes
Analysis Type DetailLC-MS
Release Date2022-12-24
Release Version1
Shiyang Song Shiyang Song
https://dx.doi.org/10.21228/M8JX2X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA177718KO_CD_3KO_CD Rev-erb cardiomyocyte specific knock out heart ventrcle harvest from KO mouse fed with chow diet
SA177719KO_CD_2KO_CD Rev-erb cardiomyocyte specific knock out heart ventrcle harvest from KO mouse fed with chow diet
SA177720KO_CD_1KO_CD Rev-erb cardiomyocyte specific knock out heart ventrcle harvest from KO mouse fed with chow diet
SA177715KO-HFHSD_2KO-HFHSD Rev-erb cardiomyocyte specific knock out heart ventrcle harvest from KOmouse fed with high fat high sucrose diet
SA177716KO-HFHSD_3KO-HFHSD Rev-erb cardiomyocyte specific knock out heart ventrcle harvest from KOmouse fed with high fat high sucrose diet
SA177717KO-HFHSD_1KO-HFHSD Rev-erb cardiomyocyte specific knock out heart ventrcle harvest from KOmouse fed with high fat high sucrose diet
SA177721WT_CD_2WT_CD wild type control heart ventrcle harvest from WT mouse fed with chow diet
SA177722WT_CD_3WT_CD wild type control heart ventrcle harvest from WT mouse fed with chow diet
SA177723WT_CD_1WT_CD wild type control heart ventrcle harvest from WT mouse fed with chow diet
SA177724WT_HFHSD_1WT_HFHSD wild type control heart ventrcle harvest from WT mouse fed with high fat high sucrose diet
SA177725WT_HFHSD_2WT_HFHSD wild type control heart ventrcle harvest from WT mouse fed with high fat high sucrose diet
SA177726WT_HFHSD_3WT_HFHSD wild type control heart ventrcle harvest from WT mouse fed with high fat high sucrose diet
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.

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 Other
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: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
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