Summary of Study ST002958

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 PR001840. The data can be accessed directly via it's Project DOI: 10.21228/M8W13F 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.

Study ID	ST002958
Study Title	Lipidomic analysis of demyelination and remyelination in the Plp1-iCKO-Myrf mouse model of demyelination
Study Summary	In this study, we obtained a longitudinal lipidomic profile of the brain, spinal cord, and serum using a genetic mouse model of demyelination, known as Plp1-iCKO-Myrf mice. This model has distinct phases of demyelination and remyelination over the course of 24 weeks, in which loss of motor function peaks during demyelination.
Institute	University of Kansas
Last Name	Hartley
First Name	Meredith
Address	2030 Becker Drive, Room 220F
Email	hartley@ku.edu
Phone	7858641782
Submit Date	2023-10-31
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2023-11-17
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001840
Project DOI:	doi: 10.21228/M8W13F
Project Title:	Lipidomic analysis of demyelination and remyelination in brain and spinal cord
Project Summary:	In this study, we obtained a longitudinal lipidomic profile of the brain, spinal cord, and serum using a genetic mouse model of demyelination, known as Plp1-iCKO-Myrf mice. This model has distinct phases of demyelination and remyelination over the course of 24 weeks, in which loss of motor function peaks during demyelination.
Institute:	University of Kansas
Department:	Chemistry
Last Name:	Hartley
First Name:	Meredith
Address:	2030 Becker Drive, Room 220F
Email:	hartley@ku.edu
Phone:	7858641782

Subject:

Subject ID:	SU003071
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	Tissue	Genotype	Timepoint	Treatment
SA322098	QC10_brain	Brain	N/A	N/A	N/A
SA322099	QC09_brain	Brain	N/A	N/A	N/A
SA322100	QC05_brain	Brain	N/A	N/A	N/A
SA322101	QC02_brain	Brain	N/A	N/A	N/A
SA322102	QC03_brain	Brain	N/A	N/A	N/A
SA322103	QC01_brain	Brain	N/A	N/A	N/A
SA322104	QC06_brain	Brain	N/A	N/A	N/A
SA322105	QC17_brain	Brain	N/A	N/A	N/A
SA322106	QC07_brain	Brain	N/A	N/A	N/A
SA322107	QC08_brain	Brain	N/A	N/A	N/A
SA322108	IS11_brain	Brain	N/A	N/A	N/A
SA322109	IS12_brain	Brain	N/A	N/A	N/A
SA322110	QC12_brain	Brain	N/A	N/A	N/A
SA322111	QC11_brain	Brain	N/A	N/A	N/A
SA322112	QC13_brain	Brain	N/A	N/A	N/A
SA322113	QC14_brain	Brain	N/A	N/A	N/A
SA322114	QC15_brain	Brain	N/A	N/A	N/A
SA322115	IS02_brain	Brain	N/A	N/A	N/A
SA322116	IS01_brain	Brain	N/A	N/A	N/A
SA322117	IS03_brain	Brain	N/A	N/A	N/A
SA322118	IS04_brain	Brain	N/A	N/A	N/A
SA322119	IS09_brain	Brain	N/A	N/A	N/A
SA322120	IS10_brain	Brain	N/A	N/A	N/A
SA322121	QC04_brain	Brain	N/A	N/A	N/A
SA322122	IS08_brain	Brain	N/A	N/A	N/A
SA322123	IS07_brain	Brain	N/A	N/A	N/A
SA322124	IS05_brain	Brain	N/A	N/A	N/A
SA322125	IS06_brain	Brain	N/A	N/A	N/A
SA322126	QC16_brain	Brain	N/A	N/A	N/A
SA322020	231-3846_brain	Brain	+	Week 12	Control
SA322021	231-3847_brain	Brain	+	Week 12	Control
SA322022	231-3848_brain	Brain	+	Week 12	Control
SA322023	212-3751_brain	Brain	+	Week 12	Control
SA322024	231-3849_brain	Brain	+	Week 12	Control
SA322025	212-3750_brain	Brain	+	Week 12	Control
SA322026	212-3748_brain	Brain	+	Week 12	Control
SA322027	212-3749_brain	Brain	+	Week 12	Control
SA322070	234-3857_brain	Brain	-	Week 12	Control
SA322071	234-3855_brain	Brain	-	Week 12	Control
SA322072	234-3856_brain	Brain	-	Week 12	Control
SA322073	263-3953_brain	Brain	-	Week 12	Control
SA322074	263-3954_brain	Brain	-	Week 12	Control
SA322028	247-3905_brain	Brain	+	Week 12	SobAM2
SA322029	242-3893_brain	Brain	+	Week 12	SobAM2
SA322030	247-3906_brain	Brain	+	Week 12	SobAM2
SA322031	251-3921_brain	Brain	+	Week 12	SobAM2
SA322032	242-3892_brain	Brain	+	Week 12	SobAM2
SA322033	251-3924_brain	Brain	+	Week 12	SobAM2
SA322034	251-3922_brain	Brain	+	Week 12	SobAM2
SA322035	232-3854_brain	Brain	+	Week 12	SobAM2
SA322036	232-3853_brain	Brain	+	Week 12	SobAM2
SA322037	232-3852_brain	Brain	+	Week 12	SobAM2
SA322075	243-3894_brain	Brain	-	Week 12	SobAM2
SA322076	249-3916_brain	Brain	-	Week 12	SobAM2
SA322077	244-3897_brain	Brain	-	Week 12	SobAM2
SA322078	252-3929_brain	Brain	-	Week 12	SobAM2
SA322079	244-3896_brain	Brain	-	Week 12	SobAM2
SA322080	243-3895_brain	Brain	-	Week 12	SobAM2
SA322038	212-3745_brain	Brain	+	Week 18	Control
SA322039	212-3746_brain	Brain	+	Week 18	Control
SA322040	219-3785_brain	Brain	+	Week 18	Control
SA322041	212-3744_brain	Brain	+	Week 18	Control
SA322042	212-3747_brain	Brain	+	Week 18	Control
SA322043	219-3788_brain	Brain	+	Week 18	Control
SA322044	211-3742_brain	Brain	+	Week 18	Control
SA322045	211-3743_brain	Brain	+	Week 18	Control
SA322081	219-3787_brain	Brain	-	Week 18	Control
SA322082	218-3777_brain	Brain	-	Week 18	Control
SA322083	218-3779_brain	Brain	-	Week 18	Control
SA322084	219-3784_brain	Brain	-	Week 18	Control
SA322085	219-3786_brain	Brain	-	Week 18	Control
SA322086	218-3778_brain	Brain	-	Week 18	Control
SA322046	235-3858_brain	Brain	+	Week 18	SobAM2
SA322047	232-3851_brain	Brain	+	Week 18	SobAM2
SA322048	232-3850_brain	Brain	+	Week 18	SobAM2
SA322049	235-3859_brain	Brain	+	Week 18	SobAM2
SA322050	236-3864_brain	Brain	+	Week 18	SobAM2
SA322051	242-3890_brain	Brain	+	Week 18	SobAM2
SA322052	241-3889_brain	Brain	+	Week 18	SobAM2
SA322053	241-3888_brain	Brain	+	Week 18	SobAM2
SA322054	236-3865_brain	Brain	+	Week 18	SobAM2
SA322087	241-3885_brain	Brain	-	Week 18	SobAM2
SA322088	252-3925_brain	Brain	-	Week 18	SobAM2
SA322089	241-3887_brain	Brain	-	Week 18	SobAM2
SA322090	252-3927_brain	Brain	-	Week 18	SobAM2
SA322055	139-648_brain	Brain	+	Week 24	Control
SA322056	139-649_brain	Brain	+	Week 24	Control
SA322057	197-3658_brain	Brain	+	Week 24	Control
SA322058	197-3663_brain	Brain	+	Week 24	Control
SA322059	198-3660_brain	Brain	+	Week 24	Control
SA322060	206-3708_brain	Brain	+	Week 24	Control
SA322061	206-3709_brain	Brain	+	Week 24	Control
SA322091	140-652_brain	Brain	-	Week 24	Control
SA322092	139-647_brain	Brain	-	Week 24	Control
SA322093	139-646_brain	Brain	-	Week 24	Control
SA322094	197-3659_brain	Brain	-	Week 24	Control
SA322062	235-3861_brain	Brain	+	Week 6	Control
SA322063	235-3862_brain	Brain	+	Week 6	Control
SA322064	236-3866_brain	Brain	+	Week 6	Control
SA322065	235-3860_brain	Brain	+	Week 6	Control

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Collection:

Collection ID:	CO003064
Collection Summary:	Euthanasia was performed by carbon dioxide inhalation and cervical dislocation, and serum, brain, and spinal cord tissues were collected immediately, frozen on dry ice, and stored at -80 °C until processing.
Sample Type:	Brain; Spinal cord; Serum

Treatment:

Treatment ID:	TR003080
Treatment Summary:	Plp1-iCKO-Myrf mice were randomly assigned into the control or Sob-AM2 treatment groups. Both Cre negative mice, which do not lose Myrf and undergo demyelination, and Cre positive mice, which do undergo demyelination, were used in all experiments. The control group received control chow (Envigo Teklad 2016 diet) and the Sob-AM2 treatment group received chow containing 420 µg/kg chow of Sob-AM2 (nominal daily dose of 84 µg/kg body weight) starting 2 weeks after tamoxifen injections. Mice on control chow were euthanized at 4 timepoints: 6, 12, 18, and 24 weeks post-tamoxifen injections. Mice treated with Sob-AM2 were euthanized at 12 and 18 weeks post-tamoxifen.

Treatment ID:

TR003080

Treatment Summary:

Plp1-iCKO-Myrf mice were randomly assigned into the control or Sob-AM2 treatment groups. Both Cre negative mice, which do not lose Myrf and undergo demyelination, and Cre positive mice, which do undergo demyelination, were used in all experiments. The control group received control chow (Envigo Teklad 2016 diet) and the Sob-AM2 treatment group received chow containing 420 µg/kg chow of Sob-AM2 (nominal daily dose of 84 µg/kg body weight) starting 2 weeks after tamoxifen injections. Mice on control chow were euthanized at 4 timepoints: 6, 12, 18, and 24 weeks post-tamoxifen injections. Mice treated with Sob-AM2 were euthanized at 12 and 18 weeks post-tamoxifen.

Sample Preparation:

Sampleprep ID:	SP003077
Sampleprep Summary:	A modified Bligh-Dyer protocol was used to extract lipids from the brain and spinal cord tissue. Brain homogenates (either 300 mg/ml or 50 mg/ml) were prepared with ice cold water using a Bead Mill homogenizer (Bead Ruptor Elite, Omni international, USA). Spinal cord homogenates were prepared at 65 mg/ml in cold water. Immediately after homogenization, the brain homogenates were diluted with cold water (150 µL of 300 mg/ml brain homogenate was mixed with 800 µl of cold water. For the 50 mg/ml brain homogenates, 1 mL of homogenate was used directly. Spinal cord homogenates were diluted 10-fold (100 μl of the spinal cord homogenates with 900 μl of cold water). For all samples, 10 μl of the diluted homogenate was removed and stored at -80°C for protein quantification using a BCA assay. The diluted tissue homogenates were combined with a mixture of chloroform (containing 0.01% butylated hydroxytoluene, BHT): methanol: water (3:2:1) in glass tubes. After shaking and vortexing thoroughly, the mixture was centrifuged (Sorvall ST 40R Centrifuge, Thermo Fisher Scientific) at 1300 rpm for 10 minutes. The lower layer was carefully removed and saved in a glass tube. The remaining top layer was further extracted twice with 1.25 ml chloroform with 0.01% BHT; the lower layers were carefully removed and combined. The combined lower layer was then washed with 300 μl of 1 M KCl followed by 300 μl of water and vacuum dried completely (Savant SpeedVac SPD130DLX vacuum concentrator, Thermo Fisher Scientific, USA) to obtain the dried lipid extract. Serum (3 μl) was added directly to a vial containing 1.2 mL of chloroform: methanol: 300 mM ammonium acetate in water (300:665:35). The contents were mixed thoroughly, and the vials were centrifuged for 5 min at low speed in a clinical centrifuge to pellet proteins before submitting samples to the mass spectrometer.

Sampleprep ID:

SP003077

Sampleprep Summary:

A modified Bligh-Dyer protocol was used to extract lipids from the brain and spinal cord tissue. Brain homogenates (either 300 mg/ml or 50 mg/ml) were prepared with ice cold water using a Bead Mill homogenizer (Bead Ruptor Elite, Omni international, USA). Spinal cord homogenates were prepared at 65 mg/ml in cold water. Immediately after homogenization, the brain homogenates were diluted with cold water (150 µL of 300 mg/ml brain homogenate was mixed with 800 µl of cold water. For the 50 mg/ml brain homogenates, 1 mL of homogenate was used directly. Spinal cord homogenates were diluted 10-fold (100 μl of the spinal cord homogenates with 900 μl of cold water). For all samples, 10 μl of the diluted homogenate was removed and stored at -80°C for protein quantification using a BCA assay. The diluted tissue homogenates were combined with a mixture of chloroform (containing 0.01% butylated hydroxytoluene, BHT): methanol: water (3:2:1) in glass tubes. After shaking and vortexing thoroughly, the mixture was centrifuged (Sorvall ST 40R Centrifuge, Thermo Fisher Scientific) at 1300 rpm for 10 minutes. The lower layer was carefully removed and saved in a glass tube. The remaining top layer was further extracted twice with 1.25 ml chloroform with 0.01% BHT; the lower layers were carefully removed and combined. The combined lower layer was then washed with 300 μl of 1 M KCl followed by 300 μl of water and vacuum dried completely (Savant SpeedVac SPD130DLX vacuum concentrator, Thermo Fisher Scientific, USA) to obtain the dried lipid extract. Serum (3 μl) was added directly to a vial containing 1.2 mL of chloroform: methanol: 300 mM ammonium acetate in water (300:665:35). The contents were mixed thoroughly, and the vials were centrifuged for 5 min at low speed in a clinical centrifuge to pellet proteins before submitting samples to the mass spectrometer.

Combined analysis:

Analysis ID	AN004858
Analysis type	MS
Chromatography type	None (Direct infusion)
Chromatography system	Sciex 4000 QTrap
Column	none
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	ABI Sciex API 4000 QTrap
Ion Mode	POSITIVE
Units	nmol per mg tissue wt

Chromatography:

Chromatography ID:	CH003667
Instrument Name:	Sciex 4000 QTrap
Column Name:	none
Column Temperature:	none
Flow Gradient:	none
Flow Rate:	none
Solvent A:	none
Solvent B:	none
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS004602
Analysis ID:	AN004858
Instrument Name:	ABI Sciex API 4000 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	see Mass_Spectrometry_Parameters.xlsx
Ion Mode:	POSITIVE
Acquisition Parameters File:	Mass_Spectrometry_Parameters.xlsx