Summary of Study ST003280
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 PR002032. The data can be accessed directly via it's Project DOI: 10.21228/M8ZC0C 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 | ST003280 |
| Study Title | Metabolomic analysis of Axon Regeneration in Xenopus laevis Optic Nerve |
| Study Summary | We profile the metabolite changes in the optic nerve of a transgenic line of 1 year old Xenopus laevis Tg(islet2b:gfp) frogs that either had a monocular surgery of either a left optic crush injury (crush) or sham surgery (sham). The matching controls of uninjured right optic nerves were also collected (control). Tg(islet2b:gfp) frogs were allowed to recover for 12 and 27 days post optic nerve crush. Following euthanasia, the tissues were collected for metabolomic analysis. Samples were pooled for each category (crush, sham, and control) at n =3 to obtain sufficient metabolite concentrations for analysis. 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 | 2024-06-11 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-07-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005373 | AN005374 |
|---|---|---|
| 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: | CH004072 |
| Chromatography Summary: | Positive ion mode |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore Amide HILIC (150 x 2.1mm, 2.6um) |
| Column Temperature: | 35 C |
| Flow Gradient: | The gradient began at 1.0% B for 1 min, then shifted to 95.0% B for 9 minutes, then stayed at 95.0% B for 1 min before ramping down quickly to 1.0% B for 5 minutes. |
| 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 |
| Chromatography ID: | CH004073 |
| Chromatography Summary: | Negative ion mode |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore Amide HILIC (150 x 2.1mm, 2.6um) |
| Column Temperature: | 35 C |
| Flow Gradient: | The gradient began at 1.0% B for 1 min, then shifted to 95.0% B for 9 minutes, then stayed at 95.0% B for 1 min before ramping down quickly to 1.0% B for 5 minutes. |
| Flow Rate: | 0.5 ml/min |
| Solvent A: | 95% acetonitrile/5% water; 10mM Ammonium Acetate; 0.1% acetic acid |
| Solvent B: | 50% acetonitrile/50% water; 10mM Ammonium Acetate; 0.1% acetic acid |
| Chromatography Type: | HILIC |
