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 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
Analysis ID | AN004519 | AN004520 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | HILIC | HILIC |
Chromatography system | Thermo Vanquish | Thermo Vanquish |
Column | Thermo Accucore Amide HILIC (150 x 2.1mm, 2.6um) | Thermo Accucore Amide HILIC (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: | CH003394 |
Chromatography Summary: | Mobile Phases: NEG A: 10mM Ammonium Acetate in 95% ACN w/ .1% acetic acid NEG B: 10mM Ammonium Acetate in 50% ACN w/ .1% acetic acid POS A: 10mM Ammonium Formate in 95% ACN w/ .1% formic acid POS B: 10mM Ammonium Formate in 50% ACN w/ .1% formic acid |
Instrument Name: | Thermo Vanquish |
Column Name: | Thermo Accucore Amide HILIC (150 x 2.1mm, 2.6um) |
Column Temperature: | 35 C |
Flow Gradient: | PumpModule.Pump.Pump_Pressure.AcqOn 0.000 [min] Run PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 1.0 [%] PumpModule.Pump.Curve: 5 1.000 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 1.0 [%] PumpModule.Pump.Curve: 5 9.000 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 95.0 [%] PumpModule.Pump.Curve: 5 10.000 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 95.0 [%] PumpModule.Pump.Curve: 5 10.500 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 1.0 [%] PumpModule.Pump.Curve: 5 15.000 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 1.0 [%] PumpModule.Pump.Curve: 5 15.000 [min] Stop Run |
Flow Rate: | 0.5 ml/min |
Solvent A: | 95% acetonitrile/5% water; 10mM Ammonium Formate; 0.1% formic acid |
Solvent B: | 50% acetonitrile/50% water; 10mM Ammonium Formate; 0.1% formic acid |
Chromatography Type: | HILIC |