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
Email	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:

Project:

Project ID:	PR001554
Project DOI:	doi: 10.21228/M8TM6T
Project Title:	Mass spectrometry dataset of LC-MS Lipidomics Analysis of Xenopus Laevis Optic Nerve
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 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
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:	SU002503
Subject Type:	Other organism
Subject Species:	Xenopus laevis
Taxonomy ID:	8355

Factors:

Subject type: Other organism; Subject species: Xenopus laevis (Factor headings shown in green)

mb_sample_id	local_sample_id	Factor
SA241950	CTL_R-ON_18_dpi_B2	Control
SA241951	CTL_R-ON_18_dpi_B1	Control
SA241952	CTL_R-ON_18_dpi_B3	Control
SA241953	CTL_R-ON_18_dpi_C1	Control
SA241954	CTL_R-ON_18_dpi_C2	Control
SA241955	CTL_R-ON_18_dpi_A3	Control
SA241956	CTL_R-ON_18_dpi_A1	Control
SA241957	CTL_R-ON_12_dpi_C1	Control
SA241958	CTL_R-ON_12_dpi_C2	Control
SA241959	CTL_R-ON_12_dpi_C3	Control
SA241960	CTL_R-ON_18_dpi_B4	Control
SA241961	CTL_R-ON_18_dpi_C3	Control
SA241962	CTL_R-ON_18_dpi_D1	Control
SA241963	CTL_R-ON_27_dpi_C1	Control
SA241964	CTL_R-ON_27_dpi_C2	Control
SA241965	CTL_R-ON_27_dpi_C3	Control
SA241966	CTL_R-ON_27_dpi_D1	Control
SA241967	CTL_R-ON_27_dpi_B3	Control
SA241968	CTL_R-ON_27_dpi_B2	Control
SA241969	CTL_R-ON_27_dpi_A1	Control
SA241970	CTL_R-ON_27_dpi_A2	Control
SA241971	CTL_R-ON_27_dpi_A3	Control
SA241972	CTL_R-ON_27_dpi_B1	Control
SA241973	CTL_R-ON_12_dpi_B3	Control
SA241974	CTL_R-ON_18_dpi_A2	Control
SA241975	CTL_R-ON_7_dpi_B1	Control
SA241976	CTL_R-ON_7_dpi_A2	Control
SA241977	CTL_R-ON_7_dpi_B2	Control
SA241978	CTL_R-ON_7_dpi_B3	Control
SA241979	CTL_R-ON_12_dpi_B2	Control
SA241980	CTL_R-ON_7_dpi_A1	Control
SA241981	CTL_R-ON_7_dpi_A3	Control
SA241982	CTL_R-ON_12_dpi_A3	Control
SA241983	CTL_R-ON_12_dpi_A2	Control
SA241984	CTL_R-ON_12_dpi_B1	Control
SA241985	CX_L-ON_27_dpi_A2	Crush
SA241986	CX_L-ON_27_dpi_C1	Crush
SA241987	CX L-ON_27_dpi_B3	Crush
SA241988	CX_L-ON_27_dpi_A3	Crush
SA241989	CX_L-ON_27_dpi_C2	Crush
SA241990	CX_L-ON_27_dpi_B1	Crush
SA241991	CX_L-ON_27_dpi_D1	Crush
SA241992	CX_L-ON_7_dpi_B1	Crush
SA241993	CX_L-ON_7_dpi_B3	Crush
SA241994	CX_L-ON_7_dpi_A3	Crush
SA241995	CX_L-ON_27_dpi_A1	Crush
SA241996	CX_L-ON_7_dpi_B2	Crush
SA241997	CX_L-ON_7_dpi_A2	Crush
SA241998	CX_L-ON_27_dpi_C3	Crush
SA241999	CX_L-ON_27_dpi_B2	Crush
SA242000	CX_L-ON_18_dpi_B2	Crush
SA242001	CX_L-ON_18_dpi_B3	Crush
SA242002	CX_L-ON_18_dpi_C1	Crush
SA242003	CX_L-ON_18_dpi_C2	Crush
SA242004	CX_L-ON_18_dpi_B1	Crush
SA242005	CX_L-ON_12_dpi_A1	Crush
SA242006	CX_L-ON_18_dpi_B4	Crush
SA242007	CX_L-ON_18_dpi_A1	Crush
SA242008	CX_L-ON_18_dpi_A2	Crush
SA242009	CX_L-ON_18_dpi_C3	Crush
SA242010	CX_L-ON_18_dpi_A3	Crush
SA242011	CX_L-ON_12_dpi_B1	Crush
SA242012	CX_L-ON_12_dpi_A3	Crush
SA242013	CX_L-ON_12_dpi_A2	Crush
SA242014	CX_L-ON_18_dpi_D1	Crush
SA242015	CX_L-ON_12_dpi_B3	Crush
SA242016	CX_L-ON_12_dpi_B2	Crush
SA242017	CX_L-ON_12_dpi_C3	Crush
SA242018	CX_L-ON_12_dpi_C2	Crush
SA242019	CX_L-ON_7_dpi_A1	Crush
SA242020	CX_L-ON_12_dpi_C1	Crush
SA242021	CTL_R-ON_Naïve_B1	Naïve
SA242022	CTL_R-ON_Naïve_B2	Naïve
SA242023	CTL_R-ON_Naïve_A2	Naïve
SA242024	CTL_R-ON_Naïve_B3	Naïve
SA242025	CX_L-ON_Naïve_A3	Naïve
SA242026	CTL_R-ON_Naïve_A1	Naïve
SA242027	CX_L-ON_Naïve_A1	Naïve
SA242028	CX_L-ON_Naïve_A2	Naïve
SA242029	CX_L-ON_Naïve_B1	Naïve
SA242030	CX_L-ON_Naïve_B3	Naïve
SA242031	Sham_R-ON_27_dpi_A3	Sham
SA242032	L-ON_Sham_18_dpi	Sham
SA242033	Sham_L-ON_27_dpi_A3	Sham
SA242034	R-ON_Sham_18_dpi	Sham

Showing results 1 to 85 of 85

Showing results 1 to 85 of 85

Collection:

Collection ID:	CO002496
Collection Summary:	Optic nerves were collected from frogs at 7, 12, 18 and 27 weeks post optic nerve crush and subjected to lipid profiling.
Sample Type:	Eye tissue

Treatment:

Treatment ID:	TR002515
Treatment Summary:	Optic nerves from each of 10 post-metamorphic transgenic Tg(Islet2b:EGFP-RPL10a) Xenopus laevis frogs, 3.5 - 5.0 cm in length, were either left untreated (naïve) or underwent a monocular surgery (operated; Fig. 1). Operated individuals were anesthetized with 0.05% ethyl 3-aminobenzoate methanesulfonate (Sigma, USA) and received either a sham surgery (sham) or a crush injury (crush) to the right optic nerve, and no treatment the left optic nerve (control; Fig. 1).

Treatment ID:

TR002515

Treatment Summary:

Optic nerves from each of 10 post-metamorphic transgenic Tg(Islet2b:EGFP-RPL10a) Xenopus laevis frogs, 3.5 - 5.0 cm in length, were either left untreated (naïve) or underwent a monocular surgery (operated; Fig. 1). Operated individuals were anesthetized with 0.05% ethyl 3-aminobenzoate methanesulfonate (Sigma, USA) and received either a sham surgery (sham) or a crush injury (crush) to the right optic nerve, and no treatment the left optic nerve (control; Fig. 1).

Sample Preparation:

Sampleprep ID:	SP002509
Sampleprep Summary:	Lipids were extracted from the optic nerve 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.

Sampleprep ID:

SP002509

Sampleprep Summary:

Lipids were extracted from the optic nerve 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	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

MS:

MS ID:	MS003673
Analysis ID:	AN003935
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:	UNSPECIFIED