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MB Sample ID: SA100923
Local Sample ID: | PR_NC_PS_OD_905 |
Subject ID: | SU001455 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001455 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
PR_NC_PS_OD_905 | SA100923 | FL014200 | Thy1-ChR2-EYFP | Genotype |
PR_NC_PS_OD_905 | SA100923 | FL014200 | No Crush, light stimulation | Treatment |
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 |