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 |
| 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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Collection:
| Collection ID: | CO002875 |
| Collection Summary: | In the tissue collection process, mice were euthanized using an overdose of MS-222. The optic nerve was removed via dissection from the optic nerve head to the optic chiasm. The retinas of both female and male Zebrafish were collected and separated into biological samples. Due to the small tissue and metabolomics resolution constraints, optic nerves were pooled to generate higher signal intensities. A total of 10-11 and 12 retinas were pooled from female and male zebrafish samples, respectively. The untreated retinas were pooled using the same protocol. |
| Sample Type: | Eye tissue |
