Summary of Study ST002776
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 | ST002776 |
Study Title | Zebrafish Optic Nerve Regeneration, Tectum Metabolomics - 3 Days Post Crush |
Study Summary | Optic nerve crush provides insight into the metabolome of the tectum. Regenerative model organisms provide key information regarding treatment degeneration in mammalian species; specifically, Zebrafish (Danio Rerio) have the capacity for successful adult optic nerve regeneration. Mammals, however, lack this intrinsic ability and undergo irreversible neurodegeneration seen in glaucoma, diabetes and other optic neuropathies. Optic nerve regeneration as well as the tectum metabolome are often studied to enhance regenerative research. Untargeted metabolomic studies within successful regenerative models are deficient. Evaluation of tectum tissue metabolomic changes in active zebrafish 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 tecta were collected three days after. Contralateral, uninjured optic nerve tecta 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. Optic nerve 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 |
sbhattacharya@med.miami.edu | |
Phone | 3054824103 |
Submit Date | 2023-06-29 |
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: | TR002892 |
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. |