Summary of Study ST003226

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 PR002011. The data can be accessed directly via it's Project DOI: 10.21228/M8P23X This work is supported by NIH grant, U2C- DK119886.

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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 IDST003226
Study TitleLipidomic analysis of Axon Regeneration in Xenopus laevis Retina
Study SummaryCNS injuries of the anuran amphibian, Xenopus laevis, are uniquely befitted for studying the molecular compositions of neuronal regeneration of retinal ganglion cells (RGC) due to a functional recovery of optic axons disparate to adult mammalian analogues. RGCs and their optic nerve axons undergo irreversible neurodegeneration in glaucoma and associated optic neuropathies, resulting in blindness in mammals. Conversely, Xenopus demonstrates RGC lifetime-spanning regenerative capabilities after optic nerve crush, inciting opportunities to compare de novo regeneration and develop efficient pharmaceutical approaches for vision restoration. Studies revealing lipidome alterations during optic nerve regeneration are sparse and could serve as a solid foundation for these underlying molecular changes. We profile the lipid changes in a transgenic line of 1 year old Xenopus laevis Tg(islet2b:gfp) frogs that were either had a monocular surgery of either a left optic crush injury (crush) or sham surgery (sham). The matching controls of uninjured right optic nerves were also collected (control). Tg(islet2b:gfp) frogs were allowed to recover for 12 and 27 days post optic nerve crush. Following euthanasia, the optic nerves were collected for lipidomic analysis. A modified Bligh and Dyer method was used for lipid extraction, followed by untargeted mass spectrometry lipid profiling with a Q-Exactive Orbitrap Liquid Chromatography-Mass Spectrometer (LC MS-MS) coupled with Vanquish Horizon Binary UHPLC LC-MS system.
Institute
University of Miami
Last NameBhattacharya
First NameSanjoy
Address1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Emailsbhattacharya@med.miami.edu
Phone3054824103
Submit Date2024-01-16
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-06-24
Release Version1
Sanjoy Bhattacharya Sanjoy Bhattacharya
https://dx.doi.org/10.21228/M8P23X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Sample Preparation:

Sampleprep ID:SP003352
Sampleprep Summary:Lipids were extracted from the retinal tissue with a Bligh and Dyer method. The organic phase containing the lipids was removed after centrifugation and dried down with a vacuum centrifuge. The lipids were flushed with argon gas to prevent oxidation and stored at -80°C prior to analysis. Dried lipid samples were reconstitued in 49µl of isopropanol:acetonitrile 1:1 (v/v) and 1µl of EquiSPLASH™ LIPIDOMIX® Quantitative Internal Standard (330731) and sonicated for 15 minutes for total solubilization. Samples were split into two separate vials containing 25µl each, one for positive mode and one for negative mode. Reversed phase chromatographic separation was performed on Vanquish Horizon UHPLC system (Thermo) using an Accucore Vanuqish C18+ UHPLC Column. An injection volume of 5µl was used and the flow rate was 260 µl/min. Mobile phase A was 50% acetonitrile, 50% water, 5mM ammonium formate, and 0.1% formic acid. Mobile phase B was 88% isopropanol, 10% acetonitrile, 2% water, 5mM ammonium formate and 0.1% formic acid.
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