Summary of Study ST003225

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 IDST003225
Study TitleLipidomic analysis of Axon Regeneration in Xenopus laevis Chiasm
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 Date2023-12-05
Raw Data AvailableYes
Raw Data File Type(s)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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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:SU003344
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
SA35233212dpi_Chiasm_2Optic chiasm Crush
SA35233327dpi_Chiasm_1Optic chiasm Crush
SA35233412dpi_Chiasm_1Optic chiasm Crush
SA35233527dpi_Chiasm_2Optic chiasm Crush
SA352336Sham_Chiasm_2Optic chiasm Sham
SA352337Sham_Chiasm_1Optic chiasm Sham
Showing results 1 to 6 of 6

Collection:

Collection ID:CO003337
Collection Summary:Optic chiasms were collected from frogs at 12 and 27 weeks post optic nerve crush and subjected to lipid profiling.
Sample Type:Eye tissue

Treatment:

Treatment ID:TR003353
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:SP003351
Sampleprep Summary:Lipids were extracted from the optic chiasm 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 AN005287 AN005288
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 area Peak area

Chromatography:

Chromatography ID:CH003999
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:MS005017
Analysis ID:AN005287
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:MS005018
Analysis ID:AN005288
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
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