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

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Download all metabolite data  |  Download mwTab file (Text format)   |  Download mwTab file (JSON format)   |  Download data (Contains raw data)
Study IDST001381
Study TitleLipid profile Dataset of optogenetics induced optic nerve regeneration
Study SummaryUsing 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 NameBhattacharya
First NameSanjoy
Address1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Emailsbhattacharya@med.miami.edu
Phone305-482-4103
Submit Date2020-03-27
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2020-05-22
Release Version1
Sanjoy Bhattacharya Sanjoy Bhattacharya
https://dx.doi.org/10.21228/M8J967
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA100908p_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 -
SA100915PR_PC_PS_OS_581Thy1-ChR2-EYFP Crush, light stimulation
SA100916PR_PC_PS_OS_903Thy1-ChR2-EYFP Crush, light stimulation
SA100917PR_PC_PS_OS_905Thy1-ChR2-EYFP Crush, light stimulation
SA100918PR_PC_PS_OS_889Thy1-ChR2-EYFP Crush, light stimulation
SA100919PR_PC_PS_OS_777Thy1-ChR2-EYFP Crush, light stimulation
SA100920PR_PC_PS_OS_901Thy1-ChR2-EYFP Crush, light stimulation
SA100909PR_PC_NS_OS_796Thy1-ChR2-EYFP Crush, No light stimulation
SA100910PR_PC_NS_OS_791Thy1-ChR2-EYFP Crush, No light stimulation
SA100911PR_PC_NS_OS_744Thy1-ChR2-EYFP Crush, No light stimulation
SA100912PR_PC_NS_OS_607Thy1-ChR2-EYFP Crush, No light stimulation
SA100913PR_PC_NS_OS_608Thy1-ChR2-EYFP Crush, No light stimulation
SA100914PR_PC_NS_OS_806Thy1-ChR2-EYFP Crush, No light stimulation
SA100921PR_NC_PS_OD_901Thy1-ChR2-EYFP No Crush, light stimulation
SA100922PR_NC_PS_OD_889Thy1-ChR2-EYFP No Crush, light stimulation
SA100923PR_NC_PS_OD_905Thy1-ChR2-EYFP No Crush, light stimulation
SA100924PR_NC_PS_OD_581Thy1-ChR2-EYFP No Crush, light stimulation
SA100925PR_NC_PS_OD_613Thy1-ChR2-EYFP No Crush, light stimulation
SA100926PR_NC_PS_OD_777Thy1-ChR2-EYFP No Crush, light stimulation
SA100927PR_NC_NS_OD_607Thy1-ChR2-EYFP No Crush, No light stimulation
SA100928PR_NC_NS_OD_608Thy1-ChR2-EYFP No Crush, No light stimulation
SA100929PR_NC_NS_OD_796Thy1-ChR2-EYFP No Crush, No light stimulation
SA100930PR_NC_NS_OD_793Thy1-ChR2-EYFP No Crush, No light stimulation
SA100931PR_NC_NS_OD_791Thy1-ChR2-EYFP No Crush, No light stimulation
SA100932PR_NC_NS_OD_744Thy1-ChR2-EYFP No Crush, No light stimulation
SA100907NR_PC_PS_OS_519- -
SA100939NR_PC_PS_OS_616Wild-type Crush, light stimulation
SA100940NR_PC_PS_OS_518Wild-type Crush, light stimulation
SA100941NR_PC_PS_OS_549Wild-type Crush, light stimulation
SA100942NR_PC_PS_OS_539Wild-type Crush, light stimulation
SA100943NR_PC_PS_OS_579Wild-type Crush, light stimulation
SA100933NR_PC_NS_OS_766Wild-type Crush, No light stimulation
SA100934NR_PC_NS_OS_540Wild-type Crush, No light stimulation
SA100935NR_PC_NS_OS_601Wild-type Crush, No light stimulation
SA100936NR_PC_NS_OS_603Wild-type Crush, No light stimulation
SA100937NR_PC_NS_OS_604Wild-type Crush, No light stimulation
SA100938NR_PC_NS_OS_782Wild-type Crush, No light stimulation
SA100944NR_NC_PS_OD_519Wild-type No Crush, light stimulation
SA100945NR_NC_PS_OD_518Wild-type No Crush, light stimulation
SA100946NR_NC_PS_OD_549Wild-type No Crush, light stimulation
SA100947NR_NC_PS_OD_552Wild-type No Crush, light stimulation
SA100948NR_NC_PS_OD_579Wild-type No Crush, light stimulation
SA100949NR_NC_PS_OD_616Wild-type No Crush, light stimulation
SA100950NR_NC_NS_OD_603Wild-type No Crush, No light stimulation
SA100951NR_NC_NS_OD_602Wild-type No Crush, No light stimulation
SA100952NR_NC_NS_OD_614Wild-type No Crush, No light stimulation
SA100953NR_NC_NS_OD_766Wild-type No Crush, No light stimulation
SA100954NR_NC_NS_OD_540Wild-type No Crush, No light stimulation
SA100955NR_NC_NS_OD_742Wild-type No Crush, No light stimulation

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