PXD032788

PXD032788 is an original dataset announced via ProteomeXchange.

Title	Labeled quantitative proteomics dataset of optogenetics induced axon regeneration
Description	This labeled quantitative proteomics dataset was collected from a transgenic channel rhodopsin mouse model (Chr2) subjected to light stimulation after traumatic optic nerve crush (ONC) was performed. Mouse models expressing channel rhodopsin were subjected to therapeutic light stimulation promoting axon regeneration of retinal ganglion cell (RGC) axons post optic nerve crush. Experimental mice and wild type control mice were euthanized, and optic nerves were collected. A protein extraction was carried out by careful mincing of the tissue in extraction buffer (TEAB, NaCl and SDS). Protein amount normalization across samples was achieved using dot blot densitometry using ImageJ software. Samples were labelled using a modified 16plex TMT (Tandem Mass Tag) kit for quantification after overnight trypsin digestion. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS/MS). Data analysis was performed using Proteome Discoverer 2.5.
HostingRepository	PRIDE
AnnounceDate	2022-08-12
AnnouncementXML	Submission_2022-08-12_00:06:46.377.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD032788
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sanjoy Bhattacharya
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-24 13:29:49	ID requested
⏵ 1	2022-08-12 00:06:47	announced

Harvey FC, Mendoza X, Liu Y, Lee RK, Bhattacharya SK, Labeled quantitative proteomics dataset of optogenetics induced axon regeneration in mice. Data Brief, 42():108304(2022) [pubmed]

submitter keyword: Axon regeneration, optogenetic stimulation, rhythmic light stimulation, quantitative proteome

Sanjoy K Bhattacharya
contact affiliation	University of Miami Miller School of Medicine, Department of Ophthalmology, Miami Integrative Metabolomics Research Center, Bascom Palmer Eye Institute (McKnight Vision Research Center)
contact email	sbhattacharya@med.miami.edu
lab head
Sanjoy Bhattacharya
contact affiliation	Bascom Palmer Eye Institute, Department of Ophthalmology, Miller School of Medicine at University of Miami, Miami, FL 33136, USA
contact email	sbhattacharya@med.miami.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/08/PXD032788

PRIDE project URI

• PRIDE
  1. PXD032788
     1. Label: PRIDE project
     2. Name: Labeled quantitative proteomics dataset of optogenetics induced axon regeneration