Summary of Study ST002929

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 PR001822. The data can be accessed directly via it's Project DOI: 10.21228/M86H8Z 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.

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Study ID	ST002929
Study Title	Hypoxia-inducible factor-1a (HIF1a) physiology in mouse skeletal muscle
Study Summary	Hypoxia-inducible factor (HIF)-1a is continuously synthesized and degraded in normoxia, whereas during hypoxia, HIF1a stabilization restricts cellular oxygen utilization. Less is known about HIF1a function(s) and sex-specific effects during normoxia in the basal state. Since skeletal muscle is the largest protein store in mammals and protein homeostasis has high energy demands, we determined HIF1a function at baseline during normoxia in skeletal muscle with the use of untargeted metabolomics. Skeletal muscle from mice with and without skeletal muscle HIF1a deletion were harvested and analyzed using untargeted metabolomics (hydrophilic interaction (HILIC) and reverse phase liquid chromatography (RPLC) methods). We identified differentially expressed metabolites in the glycolytic and TCA cycle pathways.
Institute	Cleveland Clinic
Department	Inflammation and Immunity
Last Name	Dasarathy
First Name	Srinivasan
Address	9500 Euclid Avenue, NE4-208
Email	dasaras@ccf.org
Phone	2163799846
Submit Date	2023-04-27
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2024-10-28
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001822
Project DOI:	doi: 10.21228/M86H8Z
Project Title:	Role of hypoxia inducible factor-1a (HIF1a) in Skeletal Muscle Physiology
Project Summary:	Hypoxia-inducible factor (HIF)-1a is continuously synthesized and degraded in normoxia, whereas during hypoxia, HIF1a stabilization restricts cellular oxygen utilization. Less is known about HIF1a function(s) and sex-specific effects during normoxia in the basal state. Since skeletal muscle is the largest protein store in mammals and protein homeostasis has high energy demands, we determined HIF1a function at baseline during normoxia in skeletal muscle with the use of untargeted metabolomics.
Institute:	Cleveland Clinic
Department:	Inflammation and Immunity
Last Name:	Dasarathy
First Name:	Srinivasan
Address:	9500 Euclid Avenue
Email:	dasaras@ccf.org
Phone:	2163799846
Funding Source:	NIH

Subject:

Subject ID:	SU003042
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Age Or Age Range:	12-14 weeks
Gender:	Male and female
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Genotype	Treatment	Sex
SA318000	HIFFloxFPBS1-HILICNeg	Floxed Control	PBS	Female
SA318001	HIFFloxFPBS7-HILICPos	Floxed Control	PBS	Female
SA318002	HIFFloxFPBS6-HILICPos	Floxed Control	PBS	Female
SA318003	HIFFloxFPBS2-HILICNeg	Floxed Control	PBS	Female
SA318004	HIFFloxFPBS5-HILICPos	Floxed Control	PBS	Female
SA318005	HIFFloxFPBS6-HILICNeg	Floxed Control	PBS	Female
SA318006	HIFFloxFPBS1-C18Pos	Floxed Control	PBS	Female
SA318007	HIFFloxFPBS8-HILICNeg	Floxed Control	PBS	Female
SA318008	HIFFloxFPBS7-HILICNeg	Floxed Control	PBS	Female
SA318009	HIFFloxFPBS2-HILICPos	Floxed Control	PBS	Female
SA318010	HIFFloxFPBS5-HILICNeg	Floxed Control	PBS	Female
SA318011	HIFFloxFPBS8-HILICPos	Floxed Control	PBS	Female
SA318012	HIFFloxFPBS7-C18Pos	Floxed Control	PBS	Female
SA318013	HIFFloxFPBS8-C18Pos	Floxed Control	PBS	Female
SA318014	HIFFloxFPBS6-C18Pos	Floxed Control	PBS	Female
SA318015	HIFFloxFPBS1-HILICPos	Floxed Control	PBS	Female
SA318016	HIFFloxFPBS2-C18Pos	Floxed Control	PBS	Female
SA318017	HIFFloxFPBS1-C18Neg	Floxed Control	PBS	Female
SA318018	HIFFloxFPBS5-C18Pos	Floxed Control	PBS	Female
SA318019	HIFFloxFPBS8-C18Neg	Floxed Control	PBS	Female
SA318020	HIFFloxFPBS2-C18Neg	Floxed Control	PBS	Female
SA318021	HIFFloxFPBS6-C18Neg	Floxed Control	PBS	Female
SA318022	HIFFloxFPBS7-C18Neg	Floxed Control	PBS	Female
SA318023	HIFFloxFPBS5-C18Neg	Floxed Control	PBS	Female
SA318024	HIFFloxMPBS7-HILICPos	Floxed Control	PBS	Male
SA318025	HIFFloxMPBS8-HILICPos	Floxed Control	PBS	Male
SA318026	HIFFloxMPBS4-HILICPos	Floxed Control	PBS	Male
SA318027	HIFFloxMPBS3-HILICPos	Floxed Control	PBS	Male
SA318028	HIFFloxMPBS1-HILICNeg	Floxed Control	PBS	Male
SA318029	HIFFloxMPBS7-HILICNeg	Floxed Control	PBS	Male
SA318030	HIFFloxMPBS2-HILICPos	Floxed Control	PBS	Male
SA318031	HIFFloxMPBS8-HILICNeg	Floxed Control	PBS	Male
SA318032	HIFFloxMPBS4-HILICNeg	Floxed Control	PBS	Male
SA318033	HIFFloxMPBS3-HILICNeg	Floxed Control	PBS	Male
SA318034	HIFFloxMPBS2-HILICNeg	Floxed Control	PBS	Male
SA318035	HIFFloxMPBS8-C18Pos	Floxed Control	PBS	Male
SA318036	HIFFloxMPBS4-C18Pos	Floxed Control	PBS	Male
SA318037	HIFFloxMPBS7-C18Pos	Floxed Control	PBS	Male
SA318038	HIFFloxMPBS3-C18Pos	Floxed Control	PBS	Male
SA318039	HIFFloxMPBS1-HILICPos	Floxed Control	PBS	Male
SA318040	HIFFloxMPBS1-C18Pos	Floxed Control	PBS	Male
SA318041	HIFFloxMPBS1-C18Neg	Floxed Control	PBS	Male
SA318042	HIFFloxMPBS2-C18Pos	Floxed Control	PBS	Male
SA318043	HIFFloxMPBS8-C18Neg	Floxed Control	PBS	Male
SA318044	HIFFloxMPBS4-C18Neg	Floxed Control	PBS	Male
SA318045	HIFFloxMPBS7-C18Neg	Floxed Control	PBS	Male
SA318046	HIFFloxMPBS3-C18Neg	Floxed Control	PBS	Male
SA318047	HIFFloxMPBS2-C18Neg	Floxed Control	PBS	Male
SA318048	HIFmsdFPBS6-HILICPos	Muscle specific deletion	PBS	Female
SA318049	HIFmsdFPBS5-HILICPos	Muscle specific deletion	PBS	Female
SA318050	HIFmsdFPBS3-HILICPos	Muscle specific deletion	PBS	Female
SA318051	HIFmsdFPBS1-HILICNeg	Muscle specific deletion	PBS	Female
SA318052	HIFmsdFPBS4-HILICPos	Muscle specific deletion	PBS	Female
SA318053	HIFmsdFPBS5-HILICNeg	Muscle specific deletion	PBS	Female
SA318054	HIFmsdFPBS6-HILICNeg	Muscle specific deletion	PBS	Female
SA318055	HIFmsdFPBS2-HILICPos	Muscle specific deletion	PBS	Female
SA318056	HIFmsdFPBS4-HILICNeg	Muscle specific deletion	PBS	Female
SA318057	HIFmsdFPBS3-HILICNeg	Muscle specific deletion	PBS	Female
SA318058	HIFmsdFPBS2-HILICNeg	Muscle specific deletion	PBS	Female
SA318059	HIFmsdFPBS1-C18Pos	Muscle specific deletion	PBS	Female
SA318060	HIFmsdFPBS5-C18Pos	Muscle specific deletion	PBS	Female
SA318061	HIFmsdFPBS6-C18Pos	Muscle specific deletion	PBS	Female
SA318062	HIFmsdFPBS4-C18Pos	Muscle specific deletion	PBS	Female
SA318063	HIFmsdFPBS3-C18Pos	Muscle specific deletion	PBS	Female
SA318064	HIFmsdFPBS1-HILICPos	Muscle specific deletion	PBS	Female
SA318065	HIFmsdFPBS1-C18Neg	Muscle specific deletion	PBS	Female
SA318066	HIFmsdFPBS2-C18Pos	Muscle specific deletion	PBS	Female
SA318067	HIFmsdFPBS6-C18Neg	Muscle specific deletion	PBS	Female
SA318068	HIFmsdFPBS2-C18Neg	Muscle specific deletion	PBS	Female
SA318069	HIFmsdFPBS5-C18Neg	Muscle specific deletion	PBS	Female
SA318070	HIFmsdFPBS4-C18Neg	Muscle specific deletion	PBS	Female
SA318071	HIFmsdFPBS3-C18Neg	Muscle specific deletion	PBS	Female
SA318072	HIFmsdMPBS8-HILICPos	Muscle specific deletion	PBS	Male
SA318073	HIFmsdMPBS1-HILICNeg	Muscle specific deletion	PBS	Male
SA318074	HIFmsdMPBS4-HILICPos	Muscle specific deletion	PBS	Male
SA318075	HIFmsdMPBS5-HILICPos	Muscle specific deletion	PBS	Male
SA318076	HIFmsdMPBS6-HILICPos	Muscle specific deletion	PBS	Male
SA318077	HIFmsdMPBS5-HILICNeg	Muscle specific deletion	PBS	Male
SA318078	HIFmsdMPBS3-HILICPos	Muscle specific deletion	PBS	Male
SA318079	HIFmsdMPBS8-HILICNeg	Muscle specific deletion	PBS	Male
SA318080	HIFmsdMPBS6-HILICNeg	Muscle specific deletion	PBS	Male
SA318081	HIFmsdMPBS4-HILICNeg	Muscle specific deletion	PBS	Male
SA318082	HIFmsdMPBS3-HILICNeg	Muscle specific deletion	PBS	Male
SA318083	HIFmsdMPBS1-C18Neg	Muscle specific deletion	PBS	Male
SA318084	HIFmsdMPBS5-C18Pos	Muscle specific deletion	PBS	Male
SA318085	HIFmsdMPBS6-C18Pos	Muscle specific deletion	PBS	Male
SA318086	HIFmsdMPBS4-C18Pos	Muscle specific deletion	PBS	Male
SA318087	HIFmsdMPBS3-C18Pos	Muscle specific deletion	PBS	Male
SA318088	HIFmsdMPBS1-C18Pos	Muscle specific deletion	PBS	Male
SA318089	HIFmsdMPBS8-C18Pos	Muscle specific deletion	PBS	Male
SA318090	HIFmsdMPBS3-C18Neg	Muscle specific deletion	PBS	Male
SA318091	HIFmsdMPBS8-C18Neg	Muscle specific deletion	PBS	Male
SA318092	HIFmsdMPBS6-C18Neg	Muscle specific deletion	PBS	Male
SA318093	HIFmsdMPBS5-C18Neg	Muscle specific deletion	PBS	Male
SA318094	HIFmsdMPBS4-C18Neg	Muscle specific deletion	PBS	Male
SA318095	HIFmsdMPBS1-HILICPos	Muscle specific deletion	PBS	Male

Showing results 1 to 96 of 96

Showing results 1 to 96 of 96

Collection:

Collection ID:	CO003035
Collection Summary:	Mice were sacrificed and gastrocnemius muscle collected, flash frozen, and stored at -80deg until metabolite extraction. Metabolites were extracted from myotubes and skeletal muscle using chilled methanol containing 6 spiked heavy labeled internal standards (Choline-d13, Carnitine-d9, Betaine-d9, Creatinine-d3, Picolinic acid-d4, Hippuric acid-d5). After centrifugation at 14,000g for 20 minutes to precipitate the protein pellet, the supernatant was removed, dried, and reconstituted in 300 uL 98% water / 2% acetonitrile. LC/MS (liquid chromatography/mass spectrometry) analysis was then performed, with 2 chromatography methods (C18 and HILIC) including on pooled quality control samples.
Sample Type:	Muscle
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003051
Treatment Summary:	Osmotic pumps were filled with phosphate buffered saline (PBS) and surgically implanted in mice aged 10-12 weeks. Mice were sacrificed 28 days after implantation. These mice were in the untreated arm of a larger study comparing hyperammonemic to untreated animals. The ammonia-treated samples are not included in this data submission and will be included as part of a later submission. Only the untreated samples are included in this data submission.

Treatment ID:

TR003051

Treatment Summary:

Osmotic pumps were filled with phosphate buffered saline (PBS) and surgically implanted in mice aged 10-12 weeks. Mice were sacrificed 28 days after implantation. These mice were in the untreated arm of a larger study comparing hyperammonemic to untreated animals. The ammonia-treated samples are not included in this data submission and will be included as part of a later submission. Only the untreated samples are included in this data submission.

Sample Preparation:

Sampleprep ID:	SP003048
Sampleprep Summary:	Metabolites were extracted from myotubes and skeletal muscle using chilled methanol containing 6 spiked heavy labeled internal standards (Choline-d13, Carnitine-d9, Betaine-d9, Creatinine-d3, Picolinic acid-d4, Hippuric acid-d5). After centrifugation at 14,000g for 20 minutes to precipitate the protein pellet, the supernatant was removed, dried, and reconstituted in 300 uL 98% water / 2% acetonitrile. LC/MS (liquid chromatography/mass spectrometry) analysis was then performed, with 2 chromatography methods (C18 and HILIC) including on pooled quality control samples.

Sampleprep ID:

SP003048

Sampleprep Summary:

Metabolites were extracted from myotubes and skeletal muscle using chilled methanol containing 6 spiked heavy labeled internal standards (Choline-d13, Carnitine-d9, Betaine-d9, Creatinine-d3, Picolinic acid-d4, Hippuric acid-d5). After centrifugation at 14,000g for 20 minutes to precipitate the protein pellet, the supernatant was removed, dried, and reconstituted in 300 uL 98% water / 2% acetonitrile. LC/MS (liquid chromatography/mass spectrometry) analysis was then performed, with 2 chromatography methods (C18 and HILIC) including on pooled quality control samples.

Combined analysis:

Analysis ID	AN004803	AN004804	AN004805	AN004806
Analysis type	MS	MS	MS	MS
Chromatography type	HILIC	HILIC	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish	Thermo Vanquish	Thermo Vanquish
Column	Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)	Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)	Thermo Accucore C18 (100 x 2.1mm,2.6um)	Thermo Accucore C18 (100 x 2.1mm,2.6um)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	QTRAP	QTRAP	QTRAP	QTRAP
MS instrument name	Thermo Q Exactive Focus	Thermo Q Exactive Focus	Thermo Q Exactive Focus	Thermo Q Exactive Focus
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE
Units	relative abundance	relative abundance	relative abundance	relative abundance

Chromatography:

Chromatography ID:	CH003631
Chromatography Summary:	HILIC
Instrument Name:	Thermo Vanquish
Column Name:	Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:	40
Flow Gradient:	Time (min.) Flow Rate (mL/min) %B 0.0 0.2 100 2.0 0.2 70 4.0 0.2 60 5.5 0.2 60 10.5 0.2 50 11.5 0.2 50 12.0 0.2 100 16.0 0.2 100
Flow Rate:	0.2 mL/min
Solvent A:	100% water;10 mM ammonium acetate; 0.125% acetic acid
Solvent B:	5% water/95% acetonitrile;10 mM ammonium acetate; 0.125% acetic acid
Chromatography Type:	HILIC

Chromatography ID:	CH003632
Chromatography Summary:	C18-RPLC
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Accucore C18 (100 x 2.1mm,2.6um)
Column Temperature:	60
Flow Gradient:	Time (min.) Flow Rate (mL/min) %B 0.2 0.3 5 1.0 0.3 15 8.0 0.3 95 10.0 0.3 95 12.0 0.3 5 15.0 0.3 5
Flow Rate:	0.3 mL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004549
Analysis ID:	AN004803
Instrument Name:	Thermo Q Exactive Focus
Instrument Type:	QTRAP
MS Type:	ESI
MS Comments:	Data dependent acquisitions (DDA) on the pooled representative QC samples include MS full scans at a resolution of 120,000 and HCD MS/MS scans taken on the top 5 most abundant ions at a resolution of 30,000 with dynamic exclusion. The resolution of the MS2 scans were taken at a stepped NCE energy of 10.0, 20.0 and 30.0.
Ion Mode:	POSITIVE

MS ID:	MS004550
Analysis ID:	AN004804
Instrument Name:	Thermo Q Exactive Focus
Instrument Type:	QTRAP
MS Type:	ESI
MS Comments:	Data dependent acquisitions (DDA) on the pooled representative QC samples include MS full scans at a resolution of 120,000 and HCD MS/MS scans taken on the top 5 most abundant ions at a resolution of 30,000 with dynamic exclusion. The resolution of the MS2 scans were taken at a stepped NCE energy of 10.0, 20.0 and 30.0.
Ion Mode:	NEGATIVE

MS ID:	MS004551
Analysis ID:	AN004805
Instrument Name:	Thermo Q Exactive Focus
Instrument Type:	QTRAP
MS Type:	ESI
MS Comments:	Data dependent acquisitions (DDA) on the pooled representative QC samples include MS full scans at a resolution of 120,000 and HCD MS/MS scans taken on the top 5 most abundant ions at a resolution of 30,000 with dynamic exclusion. The resolution of the MS2 scans were taken at a stepped NCE energy of 10.0, 20.0 and 30.0.
Ion Mode:	POSITIVE

MS ID:	MS004552
Analysis ID:	AN004806
Instrument Name:	Thermo Q Exactive Focus
Instrument Type:	QTRAP
MS Type:	ESI
MS Comments:	Data dependent acquisitions (DDA) on the pooled representative QC samples include MS full scans at a resolution of 120,000 and HCD MS/MS scans taken on the top 5 most abundant ions at a resolution of 30,000 with dynamic exclusion. The resolution of the MS2 scans were taken at a stepped NCE energy of 10.0, 20.0 and 30.0.
Ion Mode:	NEGATIVE