Summary of Study ST002111
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 PR001337. The data can be accessed directly via it's Project DOI: 10.21228/M8WM52 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 | ST002111 |
| Study Title | Metabolomics dataset of optogenetic axon regenerative mouse model post optic nerve crush |
| Study Summary | This metabolite dataset was collected from bacterial channel rhodopsin expressing transgenic mouse models subjected to optic nerve crush (ONC) with subsequent stimulation with light (promoting regeneration) or non-stimulation (lacking axon regeneration). ONC retains retinal ganglion cells within the retina, while degenerating axons. In transgenic bacterial channel rhodopsin expressing cells, light stimulation promotes regeneration. Genetically matched wild-type uninjured optic nerves, or control transgenic mice, were also analyzed. Metabolites were carefully extracted from finely minced optic nerve tissue using a solvent system (initial separation using 1:1 Methanol and H2O and second extraction using 8:1:1 of Acetonitrile:Acetone:Methanol). Untargeted liquid chromatography-mass spectrometry (LC-MS/MS) profiling was performed using fractionation on a Vanquish Horizon Binary UHPLC. Subsequent analyses were performed on an inline coupled Q-Exactive Orbitrap instrument. Metabolites were identified using Compound DiscovererTM software. Statistical analysis was performed using MetaboAnalyst 5.0. |
| Institute | University of Miami |
| Department | Ophthalmology |
| Last Name | Bhattacharya |
| First Name | Sanjoy K. |
| Address | 1638 NW 10th Avenue, Room 706-A, Miami, FL 33136 |
| sbhattacharya@med.miami.edu | |
| Phone | (305) 482-4103 |
| Submit Date | 2022-03-08 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-04-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001337 |
| Project DOI: | doi: 10.21228/M8WM52 |
| Project Title: | Metabolomics dataset of optogenetic axon regenerative mouse model post optic nerve crush |
| Project Summary: | This metabolite dataset was collected from bacterial channel rhodopsin expressing transgenic mouse models subjected to optic nerve crush (ONC) with subsequent stimulation with light (promoting regeneration) or non-stimulation (lacking axon regeneration). ONC retains retinal ganglion cells within the retina, while degenerating axons. In transgenic bacterial channel rhodopsin expressing cells, light stimulation promotes regeneration. Genetically matched wild-type uninjured optic nerves, or control transgenic mice, were also analyzed. Metabolites were carefully extracted from finely minced optic nerve tissue using a solvent system (initial separation using 1:1 Methanol and H2O and second extraction using 8:1:1 of Acetonitrile:Acetone:Methanol). Untargeted liquid chromatography-mass spectrometry (LC-MS/MS) profiling was performed using fractionation on a Vanquish Horizon Binary UHPLC. Subsequent analyses were performed on an inline coupled Q-Exactive Orbitrap instrument. Metabolites were identified using Compound DiscovererTM software. Statistical analysis was performed using MetaboAnalyst 5.0. |
| Institute: | University of Miami |
| Department: | Ophthalmology |
| Last Name: | Bhattacharya |
| First Name: | Sanjoy K. |
| Address: | 1638 NW 10th Avenue, Room 706-A, Miami, FL 33136 |
| Email: | sbhattacharya@med.miami.edu |
| Phone: | (305) 482-4103 |
Subject:
| Subject ID: | SU002196 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA202442 | ChR_1WPC_NS_NEG_(2) | ChR 1WPC NS |
| SA202443 | ChR_1WPC_NS_NEG_(3) | ChR 1WPC NS |
| SA202444 | ChR_1WPC_NS_POS_(1) | ChR 1WPC NS |
| SA202445 | ChR_1WPC_NS_NEG_(1) | ChR 1WPC NS |
| SA202446 | ChR_1WPC_NS_POS_(2) | ChR 1WPC NS |
| SA202447 | ChR_1WPC_NS_POS_(3) | ChR 1WPC NS |
| SA202448 | ChR_1WPC_PS_POS_(1) | ChR 1WPC PS |
| SA202449 | ChR_1WPC_PS_POS_(3) | ChR 1WPC PS |
| SA202450 | ChR_1WPC_PS_NEG_(2) | ChR 1WPC PS |
| SA202451 | ChR_1WPC_PS_NEG_(3) | ChR 1WPC PS |
| SA202452 | ChR_1WPC_PS_POS_(2) | ChR 1WPC PS |
| SA202453 | ChR_1WPC_PS_NEG_(1) | ChR 1WPC PS |
| SA202454 | ChR_2WPC_NS_POS_(3) | ChR 2WPC NS |
| SA202455 | ChR_2WPC_NS_NEG_(2) | ChR 2WPC NS |
| SA202456 | ChR_2WPC_NS_NEG_(3) | ChR 2WPC NS |
| SA202457 | ChR_2WPC_NS_POS_(1) | ChR 2WPC NS |
| SA202458 | ChR_2WPC_NS_POS_(2) | ChR 2WPC NS |
| SA202459 | ChR_2WPC_NS_NEG_(1) | ChR 2WPC NS |
| SA202460 | ChR_2WPC_PS_POS_(2) | ChR 2WPC PS |
| SA202461 | ChR_2WPC_PS_POS_(1) | ChR 2WPC PS |
| SA202462 | ChR_2WPC_PS_NEG_(2) | ChR 2WPC PS |
| SA202463 | ChR_2WPC_PS_NEG_(3) | ChR 2WPC PS |
| SA202464 | ChR_2WPC_PS_POS_(3) | ChR 2WPC PS |
| SA202465 | ChR_2WPC_PS_NEG_(1) | ChR 2WPC PS |
| SA202466 | ChR_NC_NS_POS_(8) | ChR NC NS |
| SA202467 | ChR_NC_NS_NEG_(2) | ChR NC NS |
| SA202468 | ChR_NC_NS_POS_(4) | ChR NC NS |
| SA202469 | ChR_NC_NS_POS_(5) | ChR NC NS |
| SA202470 | ChR_NC_NS_POS_(2) | ChR NC NS |
| SA202471 | ChR_NC_NS_NEG_(3) | ChR NC NS |
| SA202472 | ChR_NC_NS_NEG_(4) | ChR NC NS |
| SA202473 | ChR_NC_NS_NEG_(8) | ChR NC NS |
| SA202474 | ChR_NC_NS_POS_(3) | ChR NC NS |
| SA202475 | ChR_NC_NS_NEG_(7) | ChR NC NS |
| SA202476 | ChR_NC_NS_NEG_(6) | ChR NC NS |
| SA202477 | ChR_NC_NS_NEG_(5) | ChR NC NS |
| SA202478 | ChR_NC_NS_POS_(6) | ChR NC NS |
| SA202479 | ChR_NC_NS_NEG_(1) | ChR NC NS |
| SA202480 | ChR_NC_NS_POS_(7) | ChR NC NS |
| SA202481 | ChR_NC_NS_POS_(1) | ChR NC NS |
| SA202482 | WT_1WPC_NS_POS_(4) | WT 1WPC NS |
| SA202483 | WT_1WPC_NS_POS_(3) | WT 1WPC NS |
| SA202484 | WT_1WPC_NS_NEG_(4) | WT 1WPC NS |
| SA202485 | WT_1WPC_NS_NEG_(3) | WT 1WPC NS |
| SA202486 | WT_1WPC_NS_NEG_(1) | WT 1WPC NS |
| SA202487 | WT_1WPC_NS_NEG_(2) | WT 1WPC NS |
| SA202488 | WT_1WPC_NS_POS_(2) | WT 1WPC NS |
| SA202489 | WT_1WPC_NS_POS_(1) | WT 1WPC NS |
| SA202490 | WT_2WPC_NS_NEG_(1) | WT 2WPC NS |
| SA202491 | WT_2WPC_NS_POS_(3) | WT 2WPC NS |
| SA202492 | WT_2WPC_NS_POS_(1) | WT 2WPC NS |
| SA202493 | WT_2WPC_NS_POS_(2) | WT 2WPC NS |
| SA202494 | WT_2WPC_NS_NEG_(3) | WT 2WPC NS |
| SA202495 | WT_2WPC_NS_NEG_(2) | WT 2WPC NS |
| SA202496 | WT_NC_NS_NEG_(5) | WT NC NS |
| SA202497 | WT_NC_NS_NEG_(6) | WT NC NS |
| SA202498 | WT_NC_NS_NEG_(2) | WT NC NS |
| SA202499 | WT_NC_NS_NEG_(4) | WT NC NS |
| SA202500 | WT_NC_NS_NEG_(3) | WT NC NS |
| SA202501 | WT_NC_NS_POS_(1) | WT NC NS |
| SA202502 | WT_NC_NS_POS_(5) | WT NC NS |
| SA202503 | WT_NC_NS_POS_(6) | WT NC NS |
| SA202504 | WT_NC_NS_POS_(4) | WT NC NS |
| SA202505 | WT_NC_NS_POS_(3) | WT NC NS |
| SA202506 | WT_NC_NS_POS_(2) | WT NC NS |
| SA202507 | WT_NC_NS_NEG_(1) | WT NC NS |
| Showing results 1 to 66 of 66 |
Collection:
| Collection ID: | CO002189 |
| Collection Summary: | Three-month-old Thy1-Chr2-eYFP and C57BL6/J mice were anesthetized by intraperitoneal injection of Ketamine/Xylazine cocktail. Before crush, eyes received topical anesthesia using 0.5/% proparacaine. A 1 mm hole in the superior-temporal conjunctiva was made, the muscle tissue was separated, and the optic nerve was exposed. The optic nerve was then crushed using Dumont #5 forceps (Fine Science Tools, Foster City, CA, USA) at approximately 0.5-1 mm behind the globe without damaging retinal vessels or affecting the blood supply. Mice of either sex were randomly assigned into either the optogenetic stimulation group or the control group. The mice in the optogenetic stimulation group received blue light stimulation (~470 nm) at 1 HZ frequency while the mice in the control group were kept in a normal 12h light/dark environment. The mice were kept in the stimulated environment one or two weeks after crush according to the experimental design. |
| Sample Type: | Eye tissue |
Treatment:
| Treatment ID: | TR002208 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP002202 |
| Sampleprep Summary: | Optic nerves from three mice were pooled per condition prior to metabolite extraction. Untargeted metabolomics was performed and analyzed using high-performance liquid chromatography and mass spectrometry using a Q-Exactive Orbitrap instrument coupled with a Vanquish Horizon Binary UHPLC LC-MS system. |
Combined analysis:
| Analysis ID | AN003454 | AN003455 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C18+ (100 x 2.1mm,1.5um) | Thermo Accucore C18+ (100 x 2.1mm,1.5um) |
| 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 | μg/mL | μg/mL |
Chromatography:
| Chromatography ID: | CH002552 |
| Chromatography Summary: | Positive Ion mode |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C18+ (100 x 2.1mm,1.5um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002553 |
| Chromatography Summary: | Negative Ion mode |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C18+ (100 x 2.1mm,1.5um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003217 |
| Analysis ID: | AN003454 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolites were identified using Compound Discoverer 3.3 software. Protein quantification was performed and resulting peak intensities were used to quantify metabolite levels. Corrected peak intensities were imported to MetaboAnalyst 5.0 for statistical analysis. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003218 |
| Analysis ID: | AN003455 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolites were identified using Compound Discoverer 3.3 software. Protein quantification was performed and resulting peak intensities were used to quantify metabolite levels. Corrected peak intensities were imported to MetaboAnalyst 5.0 for statistical analysis. |
| Ion Mode: | NEGATIVE |
