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

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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.