Summary of Study ST002706

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 PR001677. The data can be accessed directly via it's Project DOI: 10.21228/M8XQ5D 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	ST002706
Study Title	Plasma metabolomics of Bmal1-KO and Bmal1-KO+AAV
Study Summary	Disruption of the circadian clock in skeletal muscle worsens local and systemic health, leading to decreased muscle strength, metabolic dysfunction, and aging-like phenotypes. Whole-body knockout mice that lack Bmal1, a key component of the molecular clock, display premature aging. Here, by using adeno-associated viruses, we rescued Bmal1 expression specifically in the skeletal muscle of Bmal1-KO mice and found that this improves their healthspan and lifespan. Plasma samples from 40-week-old KO and KO+AAV male mice were collected at ZT1 to characterize the systemic effects of muscle-specific expression of Bmal1. Overall, our findings highlight the critical role of skeletal muscle in systemic health.
Institute	University of Florida
Last Name	Esser
First Name	Karyn
Address	1345 Center Drive, M552, Gainesville, Florida, 32610, USA
Email	kaesser@ufl.edu
Phone	352-273-5728
Submit Date	2023-05-16
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2024-05-31
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001677
Project DOI:	doi: 10.21228/M8XQ5D
Project Title:	Changes in the plasma metabolomics en in the muscle-specific rescue of Bmal1
Project Summary:	This study examines the systemic effects of muscle-specific Bmal1 expression in the Bmal1-KO mouse model. We used an adeno-associated virus to rescue the expression of the clock gene Bmal1 in skeletal muscle of the Bmal1 KO.
Institute:	University of Florida
Department:	Department of Physiology and Aging
Last Name:	Esser
First Name:	Karyn
Address:	1345 Center Drive, M552, Gainesville, Florida, 32610, USA
Email:	kaesser@ufl.edu
Phone:	352-273-5728

Subject:

Subject ID:	SU002811
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	B6.129-Arntltm1Bra/J
Age Or Age Range:	40 weeks
Gender:	Male
Animal Feed:	Ad libitum
Animal Water:	Ad libitum

Factors:

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

mb_sample_id	local_sample_id	Genotype	Treatment
SA272174	PL12	Bmal1-KO	AAV
SA272175	Pool2	Bmal1-KO	AAV
SA272176	PL11	Bmal1-KO	AAV
SA272177	PL10	Bmal1-KO	AAV
SA272178	PL9	Bmal1-KO	AAV
SA272179	PL6	Bmal1-KO	Control
SA272180	PL7	Bmal1-KO	Control
SA272181	PL8	Bmal1-KO	Control
SA272182	PL5	Bmal1-KO	Control
SA272183	Pool1	Bmal1-KO	Control

Showing results 1 to 10 of 10

Showing results 1 to 10 of 10

Collection:

Collection ID:	CO002804
Collection Summary:	Mice were anesthetized using isofluorane. Blood was collected by intracardiac puncture. EDTA was used as anticoagulant. Blood was centrifuged at 2,000xg for 15 mins and plasma was collected and subsequently frozen in liquid nitrogen. Samples are stored at -80°C.
Sample Type:	Blood (plasma)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002820
Treatment Summary:	Bmal1-KO+AAV mice were systemically infected in the subxiphoid region with 20μl containing 2 × 10^11 genome copies of AAV9 on postnatal day 5.

Sample Preparation:

Sampleprep ID:	SP002817
Sampleprep Summary:	All provided samples were extracted following our cellular extraction procedure with pre-normalization to the sample protein content. Each extract was spiked with 1 ul of standard mixture consisting of deuterium labeled carnitine, acetylcarnitine, propionylcarnitine, butyrylcarnitine, isovalerylcarnitine, octanoylcarnitine, myristoylcarnitine and palmitoylcarnitine to targeted identification of carnitines in the sample. Metabolite extraction was done by protein precipitation using 200 µl of 8:1:1 Acetonitrile: Methanol: Acetone with 0.1% formic acid. Further protein precipitation was allowed by incubating the samples at 4°C for 20 min. Samples were placed in an ultrasonic bath for 10 min and then centrifuged at 20 000 xg for 5min at 4°C to pellet the protein. 190 µl supernatant was transferred from each sample into clean tube and dried under a gentle stream of nitrogen at 30°C. The dried extracts were re-suspended with 25 µL water with 0.1% formic acid. Resuspension was allowed at 4°C for 10 -15 min then samples were centrifuged at 20000 xg for 5 min at 4°C. Supernatants were transferred into clean LC-vials for targeted LC-MS quantitation on a Thermo Q-Exactive Oribtrap mass spectrometer with Dionex UHPLC and autosampler.

Sampleprep ID:

SP002817

Sampleprep Summary:

All provided samples were extracted following our cellular extraction procedure with pre-normalization to the sample protein content. Each extract was spiked with 1 ul of standard mixture consisting of deuterium labeled carnitine, acetylcarnitine, propionylcarnitine, butyrylcarnitine, isovalerylcarnitine, octanoylcarnitine, myristoylcarnitine and palmitoylcarnitine to targeted identification of carnitines in the sample. Metabolite extraction was done by protein precipitation using 200 µl of 8:1:1 Acetonitrile: Methanol: Acetone with 0.1% formic acid. Further protein precipitation was allowed by incubating the samples at 4°C for 20 min. Samples were placed in an ultrasonic bath for 10 min and then centrifuged at 20 000 xg for 5min at 4°C to pellet the protein. 190 µl supernatant was transferred from each sample into clean tube and dried under a gentle stream of nitrogen at 30°C. The dried extracts were re-suspended with 25 µL water with 0.1% formic acid. Resuspension was allowed at 4°C for 10 -15 min then samples were centrifuged at 20000 xg for 5 min at 4°C. Supernatants were transferred into clean LC-vials for targeted LC-MS quantitation on a Thermo Q-Exactive Oribtrap mass spectrometer with Dionex UHPLC and autosampler.

Combined analysis:

Analysis ID	AN004387	AN004388
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex	Thermo Dionex
Column	ACE Excel 2 C18-PFP (100 x 2.1mm,2um)	ACE Excel 2 C18-PFP (100 x 2.1mm,2um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	Peak height	Peak height

Chromatography:

Chromatography ID:	CH003291
Chromatography Summary:	Global metabolomics profiling was performed on a Thermo Q-Exactive Oribtrap mass spectrometer with Dionex UHPLC and autosampler. Each extract was spiked with 1 ul of standard mixture consisting of deuterium labeled carnitine, acetylcarnitine, propionylcarnitine, butyrylcarnitine, isovalerylcarnitine, octanoylcarnitine, myristoylcarnitine and palmitoylcarnitine to targeted identification of carnitines in the sample. All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 2 Excel-C18 pfp, 100x2.1mm, 2um column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions.
Instrument Name:	Thermo Dionex
Column Name:	ACE Excel 2 C18-PFP (100 x 2.1mm,2um)
Column Temperature:	25°C
Flow Gradient:	-
Flow Rate:	350 µL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile
Chromatography Type:	Reversed phase
Solvent C:	-

MS:

MS ID:	MS004136
Analysis ID:	AN004387
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 18-pfp 100 x 2.1 mm, 2 µm column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions.
Ion Mode:	POSITIVE

MS ID:	MS004137
Analysis ID:	AN004388
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	All samples were analyzed in positive and negative heated electrospray ionization with a mass resolution of 35,000 at m/z 200 as separate injections. Separation was achieved on an ACE 18-pfp 100 x 2.1 mm, 2 µm column with mobile phase A as 0.1% formic acid in water and mobile phase B as acetonitrile. This is a polar embedded stationary phase that provides comprehensive coverage, but does have some limitation is the coverage of very polar species. The flow rate was 350 µL/min with a column temperature of 25°C. 4 µL was injected for negative ions and 2 µL for positive ions.
Ion Mode:	NEGATIVE