Summary of Study ST001381
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 PR000945. The data can be accessed directly via it's Project DOI: 10.21228/M8J967 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 | ST001381 |
| Study Title | Lipid profile Dataset of optogenetics induced optic nerve regeneration |
| Study Summary | Using the transgenic Chr2 mouse (Thy1-ChR2-EYFP) as a model of regeneration, we present the profile the lipid changes that occur after optic nerve crush, light stimulation and RGC growth. Thy1-ChR2-EYFP mice and controls (C57BL/6) were divided in four groups each, no crush and no stimulation, no crush and stimulation, crush and no stimulation, crush and stimulation. |
| Institute | University of Miami |
| Last Name | Bhattacharya |
| First Name | Sanjoy |
| Address | 1638 NW 10th Avenue, Room 706-A, Miami, FL 33136 |
| sbhattacharya@med.miami.edu | |
| Phone | 305-482-4103 |
| Submit Date | 2020-03-27 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-05-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000945 |
| Project DOI: | doi: 10.21228/M8J967 |
| Project Title: | Lipid profile Dataset of optogenetics induced optic nerve regeneration |
| Project Summary: | The optic nerve transfers visual information from the retina to the brain through the axons of retinal ganglion cells (RGCs). In adult mammals, optic nerve injuries and progressive degenerative diseases lead to the irreversible loss of RGCs, resulting in blindness. Optogenetic models have proved useful in manipulating the growth of RGCs through expression of Channelrhodopsins (Chr2) and light stimulation. Using the transgenic Chr2 mouse (Thy1-ChR2-EYFP) as a model of regeneration, we present the profile the lipid changes that occur after optic nerve crush, light stimulation and RGC growth. Thy1-ChR2-EYFP mice and controls (C57BL/6) were divided in four groups each, no crush and no stimulation, no crush and stimulation, crush and no stimulation, crush and stimulation. After euthanasia, the optic nerves were collected for analysis. The Bligh and Dyer method was used for lipid extraction, followed by mass spectrometry lipid profiling on a high-resolution Q-Exactive instrument. |
| Institute: | University of Miami |
| Last Name: | Bhattacharya |
| First Name: | Sanjoy |
| Address: | 1638 NW 10th Avenue, Room 706-A, Miami, FL 33136 |
| Email: | sbhattacharya@med.miami.edu |
| Phone: | 305-482-4103 |
Subject:
| Subject ID: | SU001455 |
| 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 | Genotype | Treatment |
|---|---|---|---|
| SA100908 | p_NR_PC_PS_OS_519_A003, p_NR_PC_PS_OS_519_A004, p_NR_PC_PS_OS_519_A005, p_NR_PC_PS_OS_519_A006" | Crush, light stimulation | - |
| SA100915 | PR_PC_PS_OS_581 | Thy1-ChR2-EYFP | Crush, light stimulation |
| SA100916 | PR_PC_PS_OS_903 | Thy1-ChR2-EYFP | Crush, light stimulation |
| SA100917 | PR_PC_PS_OS_905 | Thy1-ChR2-EYFP | Crush, light stimulation |
| SA100918 | PR_PC_PS_OS_889 | Thy1-ChR2-EYFP | Crush, light stimulation |
| SA100919 | PR_PC_PS_OS_777 | Thy1-ChR2-EYFP | Crush, light stimulation |
| SA100920 | PR_PC_PS_OS_901 | Thy1-ChR2-EYFP | Crush, light stimulation |
| SA100909 | PR_PC_NS_OS_796 | Thy1-ChR2-EYFP | Crush, No light stimulation |
| SA100910 | PR_PC_NS_OS_791 | Thy1-ChR2-EYFP | Crush, No light stimulation |
| SA100911 | PR_PC_NS_OS_744 | Thy1-ChR2-EYFP | Crush, No light stimulation |
| SA100912 | PR_PC_NS_OS_607 | Thy1-ChR2-EYFP | Crush, No light stimulation |
| SA100913 | PR_PC_NS_OS_608 | Thy1-ChR2-EYFP | Crush, No light stimulation |
| SA100914 | PR_PC_NS_OS_806 | Thy1-ChR2-EYFP | Crush, No light stimulation |
| SA100921 | PR_NC_PS_OD_901 | Thy1-ChR2-EYFP | No Crush, light stimulation |
| SA100922 | PR_NC_PS_OD_889 | Thy1-ChR2-EYFP | No Crush, light stimulation |
| SA100923 | PR_NC_PS_OD_905 | Thy1-ChR2-EYFP | No Crush, light stimulation |
| SA100924 | PR_NC_PS_OD_581 | Thy1-ChR2-EYFP | No Crush, light stimulation |
| SA100925 | PR_NC_PS_OD_613 | Thy1-ChR2-EYFP | No Crush, light stimulation |
| SA100926 | PR_NC_PS_OD_777 | Thy1-ChR2-EYFP | No Crush, light stimulation |
| SA100927 | PR_NC_NS_OD_607 | Thy1-ChR2-EYFP | No Crush, No light stimulation |
| SA100928 | PR_NC_NS_OD_608 | Thy1-ChR2-EYFP | No Crush, No light stimulation |
| SA100929 | PR_NC_NS_OD_796 | Thy1-ChR2-EYFP | No Crush, No light stimulation |
| SA100930 | PR_NC_NS_OD_793 | Thy1-ChR2-EYFP | No Crush, No light stimulation |
| SA100931 | PR_NC_NS_OD_791 | Thy1-ChR2-EYFP | No Crush, No light stimulation |
| SA100932 | PR_NC_NS_OD_744 | Thy1-ChR2-EYFP | No Crush, No light stimulation |
| SA100907 | NR_PC_PS_OS_519 | - | - |
| SA100939 | NR_PC_PS_OS_616 | Wild-type | Crush, light stimulation |
| SA100940 | NR_PC_PS_OS_518 | Wild-type | Crush, light stimulation |
| SA100941 | NR_PC_PS_OS_549 | Wild-type | Crush, light stimulation |
| SA100942 | NR_PC_PS_OS_539 | Wild-type | Crush, light stimulation |
| SA100943 | NR_PC_PS_OS_579 | Wild-type | Crush, light stimulation |
| SA100933 | NR_PC_NS_OS_766 | Wild-type | Crush, No light stimulation |
| SA100934 | NR_PC_NS_OS_540 | Wild-type | Crush, No light stimulation |
| SA100935 | NR_PC_NS_OS_601 | Wild-type | Crush, No light stimulation |
| SA100936 | NR_PC_NS_OS_603 | Wild-type | Crush, No light stimulation |
| SA100937 | NR_PC_NS_OS_604 | Wild-type | Crush, No light stimulation |
| SA100938 | NR_PC_NS_OS_782 | Wild-type | Crush, No light stimulation |
| SA100944 | NR_NC_PS_OD_519 | Wild-type | No Crush, light stimulation |
| SA100945 | NR_NC_PS_OD_518 | Wild-type | No Crush, light stimulation |
| SA100946 | NR_NC_PS_OD_549 | Wild-type | No Crush, light stimulation |
| SA100947 | NR_NC_PS_OD_552 | Wild-type | No Crush, light stimulation |
| SA100948 | NR_NC_PS_OD_579 | Wild-type | No Crush, light stimulation |
| SA100949 | NR_NC_PS_OD_616 | Wild-type | No Crush, light stimulation |
| SA100950 | NR_NC_NS_OD_603 | Wild-type | No Crush, No light stimulation |
| SA100951 | NR_NC_NS_OD_602 | Wild-type | No Crush, No light stimulation |
| SA100952 | NR_NC_NS_OD_614 | Wild-type | No Crush, No light stimulation |
| SA100953 | NR_NC_NS_OD_766 | Wild-type | No Crush, No light stimulation |
| SA100954 | NR_NC_NS_OD_540 | Wild-type | No Crush, No light stimulation |
| SA100955 | NR_NC_NS_OD_742 | Wild-type | No Crush, No light stimulation |
| Showing results 1 to 49 of 49 |
Collection:
| Collection ID: | CO001450 |
| Collection Summary: | Thy1-ChR2-EYFP mice and controls were divided in four groups each, no crush and no stimulation, no crush and stimulation, crush and no stimulation, crush and stimulation. After euthanasia, the optic nerves were collected for analysis. The Bligh and Dyer method was used for lipid extraction, followed by mass spectrometry lipid profiling on a high-resolution Q-Exactive instrument |
| Sample Type: | Optic Nerve |
Treatment:
| Treatment ID: | TR001470 |
| Treatment Summary: | To investigate the pro-growth changes, we used the a transgenic channelrhodopsin mice (Thy1-ChR2-EYFP mice) in C57BL/6Jas a model of regeneration after optic nerve crush and C57BL/6J mice as control. The Thy1-Chr2-EYFP mouse line, which has the retinal ganglion cell (RGC) expressing channelrhodopsin-2 (Chr2) and enhanced yellow fluorescent protein (EYFP) expression utilizing an internal ribosomal entry site (IRES) within the same promoter, is widely used in optogenetic stimulation studies. The optogenetic stimulation activates Chr2. For the optic nerve crush, a surgical peritomy was made behind and above the eyeball and the eye muscles were gently retracted to expose the optic nerve. Dumont #5 forceps (FST) were used to crush the optic nerve approximately 0.5-1 mm behind the globe without damaging retinal vessels or affecting the blood supply. |
Sample Preparation:
| Sampleprep ID: | SP001463 |
| Sampleprep Summary: | Lipids were extracted using chloroform, methanol and water mixture to obtain phase separation. Next we performed untargeted liquid chromatography Q-Exactive Orbitrap tandem mass spectrometry (LC-MS/MS) for lipid profiling. We then performed peak extraction, identification, relative quantification, and alignment using Lipid Search 4.1 software. |
Combined analysis:
| Analysis ID | AN002301 | AN002302 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Accela 600 | Thermo Accela 600 |
| Column | Thermo Acclaim 120 (150 x 2.1mm,3um) | Thermo Acclaim 120 (150 x 2.1mm,3um) |
| 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 | main area | main area |
Chromatography:
| Chromatography ID: | CH001691 |
| Instrument Name: | Thermo Accela 600 |
| Column Name: | Thermo Acclaim 120 (150 x 2.1mm,3um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002144 |
| Analysis ID: | AN002301 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Xcalibur software. LipidSearch for data processing. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002145 |
| Analysis ID: | AN002302 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Xcalibur software. LipidSearch for data processing. |
| Ion Mode: | NEGATIVE |
