Summary of Study ST003724

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 PR002313. The data can be accessed directly via it's Project DOI: 10.21228/M8NK0N This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST003724
Study Title	Metabolomic analysis of skeletal muscle from control WT, immobilized WT, control mFoxO1,3,4-/- and immobilized mFoxO1,3,4-/- mice.
Study Summary	The Forkhead box O (FoxO) transcription factors have been reported to be critical factors for muscle atrophy in a variety of pathological and physiological conditions, and triple-knockout of FoxO1,3,4 prevented immobilization-induced muscle atrophy in mice. To better understand the FoxO-dependent metabolic changes in skeletal muscle during immobilization, we performed a metabolomic analysis of skeletal muscle (gastrocnemius muscle) from control and 11-day immobilized 4-month-old WT (FoxO1,3,4flox/flox) male mice and age-matched mFoxO1,3,4-/- male mice using CE-TOFMS. Our data show that triple knockout of FoxO1,3,4 prevented the metabolomic remodeling in skeletal muscles caused by immobilization.
Institute	Kyoto Prefectural University
Last Name	Kamei
First Name	Yasutomi
Address	1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
Email	oyabu0507@gmail.com
Phone	+81-75-703-5661
Submit Date	2025-01-20
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-07-14
Release Version	1

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Project:

Project ID:	PR002313
Project DOI:	doi: 10.21228/M8NK0N
Project Title:	FoxO-dependent metabolomic changes in immobilization-induced muscle atrophy in mice.
Project Summary:	To better understand the FoxO-dependent metabolic changes in skeletal muscle during immobilization, we performed a metabolomic analysis of skeletal muscle (gastrocnemius muscle) from control and 11-day immobilized 4-month-old WT (FoxO1,3,4flox/flox) male mice and age-matched mFoxO1,3,4-/- male mice using CE-TOFMS.
Institute:	Kyoto Prefectural University
Last Name:	Kamei
First Name:	Yasutomi
Address:	1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
Email:	oyabu0507@gmail.com
Phone:	+81-75-703-5661

Subject:

Subject ID:	SU004169
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	B6-129SvJ mixed with C57BL/6J
Age Or Age Range:	4-month-old
Weight Or Weight Range:	46.64 g, 43.45 g, 37.64 g, and 33.4 g for control WT (FoxO1,3,4flox/flox) mice (n = 4), 36.72 g, 30.92 g, 30.86 g, 30.57 g, and 28.74 g for immobilized WT (FoxO1,3,4flox/flox) mice (n = 5), 42.79 g, 40.88 g, 37.59 g, and 34.91 g for control mFoxO1,3,4-/- mice (n = 4), and 38.09 g, 34.42 g, 34.09 g, 32.69 g, and 30.52 g for immobilized mFoxO1,3,4-/- mice (n = 5).
Gender:	Male
Animal Animal Supplier:	CLEA Japan (Tokyo, Japan)
Animal Light Cycle:	12-h light-dark cycle
Animal Feed:	CE2
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Group	Sample source	Genotype	Treatment	Time
SA464431	TKO-Cont-2	TKO-Control	Gastrocnemius muscle	FoxO1,3,4-/-	Control	-
SA464432	TKO-Cont-4	TKO-Control	Gastrocnemius muscle	FoxO1,3,4-/-	Control	-
SA464433	TKO-Cont-3	TKO-Control	Gastrocnemius muscle	FoxO1,3,4-/-	Control	-
SA464434	TKO-Cont-1	TKO-Control	Gastrocnemius muscle	FoxO1,3,4-/-	Control	-
SA464435	TKO-IM11-1	TKO-IM11	Gastrocnemius muscle	FoxO1,3,4-/-	Immobilization	11 days
SA464436	TKO-IM11-2	TKO-IM11	Gastrocnemius muscle	FoxO1,3,4-/-	Immobilization	11 days
SA464437	TKO-IM11-3	TKO-IM11	Gastrocnemius muscle	FoxO1,3,4-/-	Immobilization	11 days
SA464438	TKO-IM11-4	TKO-IM11	Gastrocnemius muscle	FoxO1,3,4-/-	Immobilization	11 days
SA464439	TKO-IM11-5	TKO-IM11	Gastrocnemius muscle	FoxO1,3,4-/-	Immobilization	11 days
SA464440	WT-Cont-4	WT-Control	Gastrocnemius muscle	FoxO1,3,4flox/flox	Control	-
SA464441	WT-Cont-2	WT-Control	Gastrocnemius muscle	FoxO1,3,4flox/flox	Control	-
SA464442	WT-Cont-3	WT-Control	Gastrocnemius muscle	FoxO1,3,4flox/flox	Control	-
SA464443	WT-Cont-1	WT-Control	Gastrocnemius muscle	FoxO1,3,4flox/flox	Control	-
SA464444	WT-IM11-2	WT-IM11	Gastrocnemius muscle	FoxO1,3,4flox/flox	Immobilization	11 days
SA464445	WT-IM11-3	WT-IM11	Gastrocnemius muscle	FoxO1,3,4flox/flox	Immobilization	11 days
SA464446	WT-IM11-4	WT-IM11	Gastrocnemius muscle	FoxO1,3,4flox/flox	Immobilization	11 days
SA464447	WT-IM11-5	WT-IM11	Gastrocnemius muscle	FoxO1,3,4flox/flox	Immobilization	11 days
SA464448	WT-IM11-1	WT-IM11	Gastrocnemius muscle	FoxO1,3,4flox/flox	Immobilization	11 days

Showing results 1 to 18 of 18

Showing results 1 to 18 of 18

Collection:

Collection ID:	CO004162
Collection Summary:	Gastrocnemius muscles from control and 11-day immobilized 4-month-old WT (FoxO1,3,4flox/flox) male mice and age-matched mFoxO1,3,4-/- male mice were collected and snap frozen in liquid nitrogen (n = 4–5 mice/group).
Sample Type:	Muscle
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR004178
Treatment Summary:	To create the immobilized model of mFoxO1,3,4-/- (triple-knockout: TKO) and control FoxO1,3,4flox/flox (wild-type: WT) male mice, we immobilized the right hindlimb of the mouse using a plastic tube and an appropriately sized 200 μL pipette tip (strong cyanoacrylate mini was used for adhesion; only a portion of the 200-μL pipette tip was glued to the leg to avoid pressure). This procedure prevented movement of the immobilized leg alone.

Treatment ID:

TR004178

Treatment Summary:

To create the immobilized model of mFoxO1,3,4-/- (triple-knockout: TKO) and control FoxO1,3,4flox/flox (wild-type: WT) male mice, we immobilized the right hindlimb of the mouse using a plastic tube and an appropriately sized 200 μL pipette tip (strong cyanoacrylate mini was used for adhesion; only a portion of the 200-μL pipette tip was glued to the leg to avoid pressure). This procedure prevented movement of the immobilized leg alone.

Sample Preparation:

Sampleprep ID:	SP004175
Sampleprep Summary:	Gastrocnemius muscles and 750 μL of 50% acetonitrile solution (v/v) (internal standard concentration: 20 μM) were added to the crushing tubes, and the sample was crushed (3,500 rpm, 60 sec × 2 times) using a crusher under cooling, and then the same volume of 50% acetonitrile solution (v/v) was further added. After the tissue was crushed, centrifugation (2,300 × g, 4°C, 5 min) was performed. After centrifugation, the supernatant was transferred to an ultrafiltration tube (Ultrafree MC PLHCC, HMT, centrifugal filter unit 5 kDa). This was centrifuged (9,100 × g, 4°C, 120 min) and subjected to ultrafiltration. The filtrate was dried and resuspended in Milli-Q water for metabolome analyses at Human Metabolome Technologies (HMT).

Sampleprep ID:

SP004175

Sampleprep Summary:

Gastrocnemius muscles and 750 μL of 50% acetonitrile solution (v/v) (internal standard concentration: 20 μM) were added to the crushing tubes, and the sample was crushed (3,500 rpm, 60 sec × 2 times) using a crusher under cooling, and then the same volume of 50% acetonitrile solution (v/v) was further added. After the tissue was crushed, centrifugation (2,300 × g, 4°C, 5 min) was performed. After centrifugation, the supernatant was transferred to an ultrafiltration tube (Ultrafree MC PLHCC, HMT, centrifugal filter unit 5 kDa). This was centrifuged (9,100 × g, 4°C, 120 min) and subjected to ultrafiltration. The filtrate was dried and resuspended in Milli-Q water for metabolome analyses at Human Metabolome Technologies (HMT).

Combined analysis:

Analysis ID	AN006644	AN006645
Chromatography ID	CH005050	CH005051
MS ID	MS006343	MS006344
Analysis type	MS	MS
Chromatography type	CE	CE
Chromatography system	Agilent 7100 CE	Agilent 7100 CE
Column	Fused silica capillary i.d. 50 μm x 80 cm	Fused silica capillary i.d. 50 μm x 80 cm
MS Type	ESI	ESI
MS instrument type	TOF	TOF
MS instrument name	Agilent 6230 TOF	Agilent 6230 TOF
Ion Mode	POSITIVE	NEGATIVE
Units	arbitrary unit	arbitrary unit

Chromatography:

Chromatography ID:	CH005050
Chromatography Summary:	The column used has a model number TSP050375 from Polymicro Technologies. Specifically, this item was purchased and then cut and processed for use.
Instrument Name:	Agilent 7100 CE
Column Name:	Fused silica capillary i.d. 50 μm x 80 cm
Column Temperature:	N/A
Flow Gradient:	N/A
Flow Rate:	N/A
Solvent A:	Cation Buffer Solution (p/n : H3301-1001)
Solvent B:	N/A
Chromatography Type:	CE

Chromatography ID:	CH005051
Chromatography Summary:	The column used has a model number TSP050375 from Polymicro Technologies. Specifically, this item was purchased and then cut and processed for use.
Instrument Name:	Agilent 7100 CE
Column Name:	Fused silica capillary i.d. 50 μm x 80 cm
Column Temperature:	N/A
Flow Gradient:	N/A
Flow Rate:	N/A
Solvent A:	Anion Buffer Solution (p/n : I3302-1023)
Solvent B:	N/A
Chromatography Type:	CE

MS:

MS ID:	MS006343
Analysis ID:	AN006644
Instrument Name:	Agilent 6230 TOF
Instrument Type:	TOF
MS Type:	ESI
MS Comments:	CE-TOFMS(Basic) positive(Cation) mode Run buffer: Cation Buffer Solution (p/n : H3301-1001) Rinse buffer: Cation Buffer Solution (p/n : H3301-1001) Sample injection: Pressure injection 50 mbar, 5 sec CE voltage: Positive, 30 kV MS ionization: ESI Positive MS capillary voltage: 4,000 V MS scan range: m/z 50-1,000 Sheath liquid: HMT Sheath Liquid (p/n : H3301-1020)
Ion Mode:	POSITIVE

MS ID:	MS006344
Analysis ID:	AN006645
Instrument Name:	Agilent 6230 TOF
Instrument Type:	TOF
MS Type:	ESI
MS Comments:	CE-TOFMS(Basic) negative(Anion) mode Run buffer: Anion Buffer Solution (p/n : I3302-1023) Rinse buffer: Anion Buffer Solution (p/n : I3302-1023) Sample injection: Pressure injection 50 mbar, 10 sec CE voltage: Positive, 30 kV MS ionization: ESI Negative MS capillary voltage: 3,500 V MS scan range: m/z 50-1,000 Sheath liquid: HMT Sheath Liquid (p/n : H3301-1020)
Ion Mode:	NEGATIVE