Summary of Study ST004446

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 PR002809. The data can be accessed directly via it's Project DOI: 10.21228/M8K55S This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST004446
Study Title	Lipidomic dataset of mouse optic nerves in a silicone oil–induced ocular hypertension mouse model.
Study Summary	We present an optic nerve lipidomic dataset derived from a 5-month-old C57BL/6J murine model of silicone oil–induced ocular hypertension, using the contralateral BSS–injected eyes as controls. Unilateral anterior chamber injection of 2–3 µL sterile silicone oil was used to produce elevated IOP (n = 12) and induce glaucomatous optic nerve injury. The fellow silicone oil control eyes received an equal volume of sterile BSS to control for injection and manipulation. Optic nerves were collected at 2 weeks (n = 6) to capture early IOP-related changes and at 8 weeks (n = 6) to capture more chronic axonal degeneration, using sex-balanced cohorts, yielding 24 nerves in total (12 SO eyes and 12 contralateral BSS eyes). Immediately after euthanasia, optic nerves were carefully dissected, snap-frozen on dry ice, and stored at −80 °C until extraction. Lipids were extracted by mechanical homogenization using a Precellys (Bertin Technologies, France) system followed by a modified Bligh and Dyer protocol with additional extraction blanks to account for the background noise and potential artifacts. QC samples were not included at the time of acquisition, as the study design and analytical workflow did not require pooled QC samples for this lipidomics study. Internal-standard normalization, extraction blanks, and replicate consistency were used to ensure data robustness. Chromatographic separation was performed on a Vanquish Horizon UHPLC system (Thermo Scientific) equipped with an Accucore Vanquish C18+ column (150 mm × 2.1 mm, 1.5 µm). Lipid species were ionized with a heated electrospray ionization (HESI) source and detected on a Q Exactive Orbitrap mass spectrometer operated in both positive- and negative-ion modes. Raw LC–MS data were processed and annotated in LipidSearch 5.1, and subsequent normalization and group/timepoint statistical analyses were performed in MetaboAnalyst 6.0 to define IOP- and time-dependent lipid remodeling in the glaucomatous optic nerve. Our results demonstrate that, under SO-induced ocular hypertension, the optic-nerve lipidome exhibits pronounced remodeling at 8 weeks but only limited changes at 2 weeks, relative to BSS controls. We identify differentially abundant lipids across multiple classes, particularly glycerophospholipids and sphingolipids, suggesting that changes in membrane composition and lipid signaling contribute to high IOP–related axonal injury. Lipids with pronounced significant lipid shifts in our dataset are priority candidates for targeted validation and mechanistic studies.
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	2025-11-11
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2026-01-12
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002809
Project DOI:	doi: 10.21228/M8K55S
Project Title:	Lipidomic dataset of mouse optic nerves in a silicone oil–induced ocular hypertension mouse model.
Project Summary:	Glaucoma, a leading cause of irreversible blindness, is characterized by progressive retinal ganglion cell (RGC) loss with optic nerve axonal degeneration. Elevated intraocular pressure (IOP) is the major risk factor promoting axon degeneration. Because lipids are integral to axonal membrane composition, and immune signaling modulation, delineating the optic nerve lipidome under IOP elevation conditions is important for defining intraocular pressure-induced molecular remodeling. Profiling the lipidome may uncover lipid pathways amenable to therapeutic targeting for axonal protection and regeneration in glaucomatous optic neuropathy and, potentially, other central nerve systems injuries. We present optic nerve lipidomic datasets generated from a 5-month-old silicone oil–induced ocular hypertension mouse model in C57BL/6J mice with equal numbers of males and females. Unilateral anterior chamber injection of sterile silicone oil (SO) was used to elevate IOP and induce glaucomatous optic nerve injury, while the contralateral eye received an equal volume of balanced salt solution (BSS) and served as the injection control. Optic nerves from SO and BSS eyes were collected at 2 weeks (early injury) and 8 weeks (established optic nerve degeneration) after intraocular injection, snap-frozen, and stored at −80 °C until lipid extraction. Each time point included n = 6 optic nerves per condition. The Bligh and Dyer method was used for lipid extraction, followed by mass spectrometry lipid profiling using reversed phase chromatographic separation performed on Vanquish Horizon ultrahigh performance liquid chromatography (UHPLC) system (Thermo Fisher Scientific, Waltham, MA) coupled to a Q-Exactive Orbitrap Liquid Chromatography Mass Spectrometer (LC/MS-MS). Data was collected in both positive and negative ion modes for each sample. The raw scans were analyzed with LipidSearch 5.1, and the statistical analysis was conducted through Metaboanalyst 6.0.
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:	SU004608
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Treatment
SA526812	2W-Blank	Blank	NA
SA526813	8W-Blank	Blank	NA
SA526814	8W-BSS-F3	Optic Nerve	BSS
SA526815	8W-BSS-F2	Optic Nerve	BSS
SA526816	8W-BSS-F1	Optic Nerve	BSS
SA526817	8W-BSS-M3	Optic Nerve	BSS
SA526818	8W-BSS-M2	Optic Nerve	BSS
SA526819	2W-BSS-M2	Optic Nerve	BSS
SA526820	2W-BSS-M1	Optic Nerve	BSS
SA526821	8W-BSS-M1	Optic Nerve	BSS
SA526822	2W-BSS-F3	Optic Nerve	BSS
SA526823	2W-BSS-M3	Optic Nerve	BSS
SA526824	2W-BSS-F2	Optic Nerve	BSS
SA526825	2W-BSS-F1	Optic Nerve	BSS
SA526826	2W-SO-M1	Optic Nerve	SO
SA526827	2W-SO-M2	Optic Nerve	SO
SA526828	2W-SO-M3	Optic Nerve	SO
SA526829	2W-SO-F3	Optic Nerve	SO
SA526830	8W-SO-M1	Optic Nerve	SO
SA526831	8W-SO-M2	Optic Nerve	SO
SA526832	8W-SO-M3	Optic Nerve	SO
SA526833	8W-SO-F1	Optic Nerve	SO
SA526834	8W-SO-F2	Optic Nerve	SO
SA526835	8W-SO-F3	Optic Nerve	SO
SA526836	2W-SO-F1	Optic Nerve	SO
SA526837	2W-SO-F2	Optic Nerve	SO

Showing results 1 to 26 of 26

Showing results 1 to 26 of 26

Collection:

Collection ID:	CO004601
Collection Summary:	5-month-old C57BL/6J mice were euthanized, and 24 optic nerves were collected from 12 mice (n = 6 per time point) at 2 and 8 weeks after SO/BSS injection, with males and females equally represented. Tissues were immediately snap-frozen and stored at −80 °C until lipid extraction.
Sample Type:	Eye tissue

Treatment:

Treatment ID:	TR004617
Treatment Summary:	Five-month-old C57BL/6J mice of both sexes were used. Under general anesthesia with intraperitoneal ketamine (73 mg/kg) and xylazine (7.3 mg/kg), and with topical 0.5% proparacaine applied to the left eye, ocular hypertension was induced by slowly injecting 2–3 µL of sterile silicone oil (SO) into the anterior chamber until was filled, taking care to avoid contact with the lens or iris. The contralateral eye received an equal volume (2–3 µL) of sterile BSS in the anterior chamber and served as the injection control. At the end of the procedure, ophthalmic erythromycin ointment was applied to protect the corneal surface and reduce the risk of corneal and conjunctival wound infection.

Treatment ID:

TR004617

Treatment Summary:

Five-month-old C57BL/6J mice of both sexes were used. Under general anesthesia with intraperitoneal ketamine (73 mg/kg) and xylazine (7.3 mg/kg), and with topical 0.5% proparacaine applied to the left eye, ocular hypertension was induced by slowly injecting 2–3 µL of sterile silicone oil (SO) into the anterior chamber until was filled, taking care to avoid contact with the lens or iris. The contralateral eye received an equal volume (2–3 µL) of sterile BSS in the anterior chamber and served as the injection control. At the end of the procedure, ophthalmic erythromycin ointment was applied to protect the corneal surface and reduce the risk of corneal and conjunctival wound infection.

Sample Preparation:

Sampleprep ID:	SP004614
Sampleprep Summary:	Lipids were extracted from the tissue using a Precellys Homogenizer followed by a Bligh and Dyer method with additional extraction blanks. 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 reconstituted in 49µl of isopropanol: acetonitrile 1:1 (v/v) and 1µl of EquiSPLASH™ LIPIDOMIX® Quantitative Internal Standard (330731), followed by a 15-minute water bath sonication for total solubilization. Reversed phase chromatographic separation was performed on a Vanquish Horizon UHPLC system (Thermo) using an Accucore Vanquish C18+ UHPLC Column (150mm x 2.1mm, 1.5µm, Thermo Scientific). An injection volume of 5µl was used, the flow rate was 0.260 mL/min, and the column temperature was set to 55°C. 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. Ionization and detection were performed with a heated electrospray ionization (HESI) source coupled to a Q Exactive Orbitrap mass spectrometer. Data was collected in both positive and negative modes for each sample. Spray voltage was 4.23kV in positive mode and 2.52 kV in negative mode. For positive and negative mode, sheath gas flow rate was 35, auxiliary gas flow rate was 15, and sweep gas was 0. Capillary temperature was 325°C and S-lens RF level was 70. The full scan range was 250 to 1200 m/z, resolution was 70,000, and microscans was 1. Automatic gain control (AGC) target was 1e6 and maximum inject time was 100ms. In dd-MS2, the resolution was 17,500, AGC target was 1e5, loop count was 10, and isolation window was 1.0m/z. Normalized collision energy (NCE) was set to 20, 30, 40, intensity threshold was 2.0e4, and dynamic exclusion was 8.0s. Lipids were identified from their raw scans using LipidSearch 5.1 software. The quantification was carried out by the internal standard classes identified and statistical analysis was performed by Metaboanalyst 6.0.

Sampleprep ID:

SP004614

Sampleprep Summary:

Lipids were extracted from the tissue using a Precellys Homogenizer followed by a Bligh and Dyer method with additional extraction blanks. 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 reconstituted in 49µl of isopropanol: acetonitrile 1:1 (v/v) and 1µl of EquiSPLASH™ LIPIDOMIX® Quantitative Internal Standard (330731), followed by a 15-minute water bath sonication for total solubilization. Reversed phase chromatographic separation was performed on a Vanquish Horizon UHPLC system (Thermo) using an Accucore Vanquish C18+ UHPLC Column (150mm x 2.1mm, 1.5µm, Thermo Scientific). An injection volume of 5µl was used, the flow rate was 0.260 mL/min, and the column temperature was set to 55°C. 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. Ionization and detection were performed with a heated electrospray ionization (HESI) source coupled to a Q Exactive Orbitrap mass spectrometer. Data was collected in both positive and negative modes for each sample. Spray voltage was 4.23kV in positive mode and 2.52 kV in negative mode. For positive and negative mode, sheath gas flow rate was 35, auxiliary gas flow rate was 15, and sweep gas was 0. Capillary temperature was 325°C and S-lens RF level was 70. The full scan range was 250 to 1200 m/z, resolution was 70,000, and microscans was 1. Automatic gain control (AGC) target was 1e6 and maximum inject time was 100ms. In dd-MS2, the resolution was 17,500, AGC target was 1e5, loop count was 10, and isolation window was 1.0m/z. Normalized collision energy (NCE) was set to 20, 30, 40, intensity threshold was 2.0e4, and dynamic exclusion was 8.0s. Lipids were identified from their raw scans using LipidSearch 5.1 software. The quantification was carried out by the internal standard classes identified and statistical analysis was performed by Metaboanalyst 6.0.

Combined analysis:

Analysis ID	AN007448	AN007449
Chromatography ID	CH005640	CH005640
MS ID	MS007140	MS007141
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:	CH005640
Chromatography Summary:	Reversed phase chromatographic separation was performed on a Vanquish Horizon UHPLC system (Thermo) using an Accucore Vanquish C18+ UHPLC Column (150mm x 2.1mm, 1.5µm, Thermo Scientific). An injection volume of 5µl was used, the flow rate was 0.260 mL/min, and the column temperature was set to 55°C. 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.
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:	MS007140
Analysis ID:	AN007448
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Ionization and detection were performed with a heated electrospray ionization (HESI) source coupled to a Q Exactive Orbitrap mass spectrometer. Data was collected in both positive and negative modes for each sample. Spray voltage was 4.23kV in positive mode and 2.52 kV in negative mode. For positive and negative mode, sheath gas flow rate was 35, auxiliary gas flow rate was 15, and sweep gas was 0. Capillary temperature was 325°C and S-lens RF level was 70. The full scan range was 250 to 1200 m/z, resolution was 70,000, and microscans was 1. Automatic gain control (AGC) target was 1e6 and maximum inject time was 100ms. In dd-MS2, the resolution was 17,500, AGC target was 1e5, loop count was 10, and isolation window was 1.0m/z. Normalized collision energy (NCE) was set to 20, 30, 40, intensity threshold was 2.0e4, and dynamic exclusion was 8.0s. Lipids were identified from their raw scans using LipidSearch 5.1 software. The quantification was carried out by the internal standard classes identified and statistical analysis was performed by Metaboanalyst 6.0.
Ion Mode:	POSITIVE

MS ID:	MS007141
Analysis ID:	AN007449
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Ionization and detection were performed with a heated electrospray ionization (HESI) source coupled to a Q Exactive Orbitrap mass spectrometer. Data was collected in both positive and negative modes for each sample. Spray voltage was 4.23kV in positive mode and 2.52 kV in negative mode. For positive and negative mode, sheath gas flow rate was 35, auxiliary gas flow rate was 15, and sweep gas was 0. Capillary temperature was 325°C and S-lens RF level was 70. The full scan range was 250 to 1200 m/z, resolution was 70,000, and microscans was 1. Automatic gain control (AGC) target was 1e6 and maximum inject time was 100ms. In dd-MS2, the resolution was 17,500, AGC target was 1e5, loop count was 10, and isolation window was 1.0m/z. Normalized collision energy (NCE) was set to 20, 30, 40, intensity threshold was 2.0e4, and dynamic exclusion was 8.0s. Lipids were identified from their raw scans using LipidSearch 5.1 software. The quantification was carried out by the internal standard classes identified and statistical analysis was performed by Metaboanalyst 6.0.
Ion Mode:	NEGATIVE