Summary of Study ST002414
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 PR001554. The data can be accessed directly via it's Project DOI: 10.21228/M8TM6T 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 | ST002414 |
| Study Title | Mass spectrometry dataset of LC-MS Lipidomics Analysis of Xenopus Laevis Optic Nerve |
| Study Summary | CNS 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 left untreated (naïve) or had a monocular surgery of either a left optic crush injury (crush) or sham surgery (sham). Matching controls of uninjured right optic nerves were also collected (control). Tg(islet2b:gfp) frogs were allowed to recover for 7,12,18, and 27 days post optic nerve crush. Following euthanasia, the optic nerves were collected for lipidomic analysis. A modified Bligh and Dyer method [PMID: 13671378] 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 Name | Bhattacharya |
| First Name | Sanjoy |
| Address | 1638 NW 10th Avenue, Room 706-A, Miami, FL 33136 |
| sbhattacharya@med.miami.edu | |
| Phone | 3054824103 |
| Submit Date | 2022-12-13 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-01-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003935 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Thermo Accucore C18 (150 x 2.1mm,2.6um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | µg/ml |
Chromatography:
| Chromatography ID: | CH002914 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C18 (150 x 2.1mm,2.6um) |
| Column Temperature: | 55 |
| Flow Gradient: | The gradient began at 10% B for 1 min, then shifted to 30% B for 1.5min, 50% for 3.5min, 60% for 10min, 80% for 2 min, 95% for 2 min, then stayed at 100% B for 6 min before ramping down to 10% B for 2 min. |
| Flow Rate: | 260 ul/min |
| Solvent A: | 50% acetonitrile/50% water; 0.1% formic acid; 5mM ammonium formate |
| Solvent B: | 88% isopropanol/10% acetonitrile/2% water; 0.1% formic acid; 5mM ammonium formate |
| Chromatography Type: | Reversed phase |
