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.
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 | ST003226 |
| Study Title | Lipidomic analysis of Axon Regeneration in Xenopus laevis Retina |
| 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 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 Name | Bhattacharya |
| First Name | Sanjoy |
| Address | 1638 NW 10th Avenue, Room 706-A, Miami, FL 33136 |
| sbhattacharya@med.miami.edu | |
| Phone | 3054824103 |
| Submit Date | 2024-01-16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-06-24 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002011 |
| Project DOI: | doi: 10.21228/M8P23X |
| Project Title: | Lipidomic analysis of Axon Regeneration in Xenopus laevis Chiasm |
| Project 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 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 |
| Department: | Ophthalmology |
| Last Name: | Bhattacharya |
| First Name: | Sanjoy K. |
| Address: | 1638 NW 10th Avenue, Room 706-A, Miami, FL 33136 |
| Email: | sbhattacharya@med.miami.edu |
| Phone: | 3054824103 |
Subject:
| Subject ID: | SU003345 |
| Subject Type: | Amphibian |
| Subject Species: | Xenopus laevis |
| Taxonomy ID: | 8355 |
Factors:
Subject type: Amphibian; Subject species: Xenopus laevis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment |
|---|---|---|---|
| SA352338 | CTL_12dpi_R_1 | Retina | Control |
| SA352339 | CTL_12dpi_R_2 | Retina | Control |
| SA352340 | CTL_27dpi_R_1 | Retina | Control |
| SA352341 | CTL_27dpi_R2 | Retina | Control |
| SA352342 | CTL_27dpi_R_3 | Retina | Control |
| SA352343 | CX_27dpi_R2 | Retina | Crush |
| SA352344 | CX_12dpi_R_1 | Retina | Crush |
| SA352345 | CX_27dpi_R3 | Retina | Crush |
| SA352346 | CX_27dpi_R_1 | Retina | Crush |
| SA352347 | CX_12dpi_R2 | Retina | Crush |
| SA352348 | Right_R_SHAM1 | Retina | Sham |
| SA352349 | L_R_Sham_2 | Retina | Sham |
| SA352350 | Left_R_SHAM1 | Retina | Sham |
| SA352351 | Right_R_Sham_2 | Retina | Sham |
| Showing results 1 to 14 of 14 |
Collection:
| Collection ID: | CO003338 |
| Collection Summary: | Retinas were collected from frogs at 12 and 27 days post optic nerve crush and subjected to lipid profiling. |
| Sample Type: | Eye tissue |
Treatment:
| Treatment ID: | TR003354 |
| Treatment Summary: | Optic nerves from each transgenic Tg(Islet2b:EGFP-RPL10a) Xenopus laevis frogs, 3.5 - 5.0 cm in length, underwent 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). Operated individuals were anesthetized with 0.05% ethyl 3-aminobenzoate methanesulfonate (Sigma, USA). |
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. |
Combined analysis:
| Analysis ID | AN005289 | AN005290 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C18 (150 x 2.1mm,2.6um) | Thermo Accucore C18 (150 x 2.1mm,2.6um) |
| 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 results | peak area |
Chromatography:
| Chromatography ID: | CH004000 |
| 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 |
MS:
| MS ID: | MS005019 |
| Analysis ID: | AN005289 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The raw scans were analysed and quantified with LipidSearch 5.0 and the statistical analysis was conducted through Metaboanalyst 5.0. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005020 |
| Analysis ID: | AN005290 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The raw scans were analysed and quantified with LipidSearch 5.0 and the statistical analysis was conducted through Metaboanalyst 5.0. |
| Ion Mode: | NEGATIVE |
