Summary of Study ST002930

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	ST002930
Study Title	Role of Hypoxia-inducible factor-1a (HIF1a)in Skeletal Muscle Physiology (C2C12 myotube model)
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 C2C12 murine myotubes with the use of untargeted metabolomics. 114 samples of extracted metabolites from cells were analyzed using LCMS. We identified that metabolites, especially those in the glycolytic pathway and TCA cycle, were differentially expressed in cells with HIF1a KO compared to WT.
Institute	Cleveland Clinic
Department	Inflamation and Immunity
Laboratory	Dasarathy Lab
Last Name	Dasarathy
First Name	Srinivasan
Address	9500 Euclid Avenue
Email	dasaras@ccf.org
Phone	2163799846
Submit Date	2023-10-05
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:	SU003043
Subject Type:	Cultured cells
Subject Species:	Mus musculus
Taxonomy ID:	10090
Age Or Age Range:	Passage 4-8
Gender:	Female
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Genotype	Treatment
SA318096	HIF KO C2C12 UnT3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG251	HIF1a KO	Untreated
SA318097	HIF KO C2C12 UnT2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG250	HIF1a KO	Untreated
SA318098	HIF KO C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG252	HIF1a KO	Untreated
SA318099	HIF KO C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG253	HIF1a KO	Untreated
SA318100	HIF KO C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG254	HIF1a KO	Untreated
SA318101	HIF KO C2C12 UnT1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG249	HIF1a KO	Untreated
SA318102	HIF KO C2C12 UnT1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS249	HIF1a KO	Untreated
SA318103	HIF KO C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS253	HIF1a KO	Untreated
SA318104	HIF KO C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS254	HIF1a KO	Untreated
SA318105	HIF KO C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS252	HIF1a KO	Untreated
SA318106	HIF KO C2C12 UnT3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS251	HIF1a KO	Untreated
SA318107	HIF KO C2C12 UnT2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS250	HIF1a KO	Untreated
SA318108	WT C2C12 UnT7 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS204	Wild-type	Untreated
SA318109	WT C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS203	Wild-type	Untreated
SA318110	WT C2C12 UnT9 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS206	Wild-type	Untreated
SA318111	WT C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS202	Wild-type	Untreated
SA318112	WT C2C12 UnT8 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS205	Wild-type	Untreated
SA318113	WT C2C12 unit1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS189	Wild-type	Untreated
SA318114	WT C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG202	Wild-type	Untreated
SA318115	WT C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG203	Wild-type	Untreated
SA318116	WT C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG201	Wild-type	Untreated
SA318117	WT C2C12 unit3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG191	Wild-type	Untreated
SA318118	WT C2C12 unit2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG190	Wild-type	Untreated
SA318119	WT C2C12 UnT7 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG204	Wild-type	Untreated
SA318120	WT C2C12 UnT8 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG205	Wild-type	Untreated
SA318121	WT C2C12 unit3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS191	Wild-type	Untreated
SA318122	WT C2C12 unit2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS190	Wild-type	Untreated
SA318123	WT C2C12 unit1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG189	Wild-type	Untreated
SA318124	WT C2C12 UnT9 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG206	Wild-type	Untreated
SA318125	WT C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS201	Wild-type	Untreated

Showing results 1 to 30 of 30

Showing results 1 to 30 of 30

Collection:

Collection ID:	CO003036
Collection Summary:	Metabolites were extracted from myotubes and skeletal muscle using chilled methanol containing 6 labeled internal standards (Betaine-d9, Carnitine-d9, Estrone-13C3, Cholesterol-13C3, Valeric acid-d9, Choline-d13). After centrifugation at 14,000g for 20 minutes to precipitate the protein pellet, the supernatant was removed, dried, and reconstituted in 5% acetonitrile. LC/MS (liquid chromatography/mass spectrometry) analysis was then performed, including on pooled quality control samples.
Sample Type:	Skeletal myotubes

Treatment:

Treatment ID:	TR003052
Treatment Summary:	Cells were not treated (Untreated, UnT)

Sample Preparation:

Sampleprep ID:	SP003049
Sampleprep Summary:	Metabolites were extracted from myotubes and skeletal muscle using chilled methanol containing 6 labeled internal standards (Betaine-d9, Carnitine-d9, Estrone-13C3, Cholesterol-13C3, Valeric acid-d9, Choline-d13). After centrifugation at 14,000g for 20 minutes to precipitate the protein pellet, the supernatant was removed, dried, and reconstituted in 5% acetonitrile. LC/MS (liquid chromatography/mass spectrometry) analysis was then performed, including on pooled quality control samples.

Sampleprep ID:

SP003049

Sampleprep Summary:

Metabolites were extracted from myotubes and skeletal muscle using chilled methanol containing 6 labeled internal standards (Betaine-d9, Carnitine-d9, Estrone-13C3, Cholesterol-13C3, Valeric acid-d9, Choline-d13). After centrifugation at 14,000g for 20 minutes to precipitate the protein pellet, the supernatant was removed, dried, and reconstituted in 5% acetonitrile. LC/MS (liquid chromatography/mass spectrometry) analysis was then performed, including on pooled quality control samples.

Combined analysis:

Analysis ID	AN004807	AN004808
Analysis type	MS	MS
Chromatography type	HILIC	HILIC
Chromatography system	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)
MS Type	ESI	ESI
MS instrument type	QTRAP	QTRAP
MS instrument name	Thermo Q Exactive Focus	Thermo Q Exactive Focus
Ion Mode	POSITIVE	NEGATIVE
Units	relative abundance	relative abundance

Chromatography:

Chromatography ID:	CH003633
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

MS:

MS ID:	MS004553
Analysis ID:	AN004807
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:	MS004554
Analysis ID:	AN004808
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