Summary of Study ST002775

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 PR001575. The data can be accessed directly via it's Project DOI: 10.21228/M83X51 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	ST002775
Study Title	Zebrafish Retina Regeneration Metabolomics - 3 Days Post Crush
Study Summary	Retinal regeneration has been at the forefront of optic research. Regenerative model organisms provide key information regarding treatment for optic nerve and retinal degeneration in mammalian species; specifically, Zebrafish (Danio Rerio) have the capacity for successful adult retinal regeneration. Mammals, however, lack this intrinsic ability and undergo irreversible neurodegeneration seen in glaucoma, diabetes and other optic neuropathies. Optic nerve and retinal regeneration are often studied using the retina obtained via optic nerve crush, a mechanical neurodegenerative model. Untargeted metabolomic studies within successful regenerative models are deficient. Evaluation of tissue metabolomic changes in active zebrafish retinal regeneration can elucidate prioritized metabolite pathways that can be targeted in mammalian systems for therapeutic development. Female and male (6 month to 1 year old) right Zebrafish (Tg(gap43:GFP)) optic nerves were crushed and the retinas were collected three days after. Contralateral, uninjured optic nerve retinas were collected as controls. The tissue was dissected from euthanized fish and frozen on dry ice. Samples were pooled for each category (female crush, female control, male crush, male control) and pooled at n = 10-12 to obtain sufficient metabolite concentrations for analysis. Retinal regeneration was verified by microscope visualization of GFP fluorescence. Metabolites were extracted using a Precellys Homogenizer and a serial extraction method: (1) 1:1 Methanol/Water and (2) 8:1:1 Acetonitrile/Methanol/Acetone. Metabolites were analyzed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) profiling using a Q-Exactive Orbitrap instrument coupled with Vanquish Horizon Binary UHPLC LC-MS system. Metabolites were identified and quantified using Compound Discoverer 3.3 and isotopic internal metabolites standards.
Institute	University of Miami
Department	McKnight - Ophthalmology
Laboratory	Bhattacharya Lab
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	2023-06-20
Num Groups	2
Total Subjects	67
Num Males	36
Num Females	31
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-08-07
Release Version	1

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Treatment:

Treatment ID:	TR002891
Treatment Summary:	For optic nerve crush, animals were deeply anesthetized in 0.033% tricaine methane-sulfonate (MS-222). The right optic nerve was exposed by gently removing the connective tissue on the dorsal half of the eye and rotating the eye ventrally out of the orbit with a number 5 forceps. A nerve crush was then performed using number 5 forceps to crush the nerve ~0.5–1 mm from the optic nerve head for 5 s. Success was observed by the generation of a translucent stripe in the nerve that completely separated two areas of white myelination with no bleeding. Fish were then revived in fresh aquatic system water in individual tanks. After 1 h the tanks were returned to the fish system and animals were maintained normally with daily feeding until 3 days post injury.

Treatment ID:

TR002891

Treatment Summary:

For optic nerve crush, animals were deeply anesthetized in 0.033% tricaine methane-sulfonate (MS-222). The right optic nerve was exposed by gently removing the connective tissue on the dorsal half of the eye and rotating the eye ventrally out of the orbit with a number 5 forceps. A nerve crush was then performed using number 5 forceps to crush the nerve ~0.5–1 mm from the optic nerve head for 5 s. Success was observed by the generation of a translucent stripe in the nerve that completely separated two areas of white myelination with no bleeding. Fish were then revived in fresh aquatic system water in individual tanks. After 1 h the tanks were returned to the fish system and animals were maintained normally with daily feeding until 3 days post injury.