Return to study ST001381 main page

MB Sample ID: SA100925

Local Sample ID:PR_NC_PS_OD_613
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 IDMB Sample IDFactor Level IDLevel ValueFactor Name
PR_NC_PS_OD_613SA100925FL014200Thy1-ChR2-EYFPGenotype
PR_NC_PS_OD_613SA100925FL014200No Crush, light stimulationTreatment

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
  logo