PXD002273

PXD002273 is an original dataset announced via ProteomeXchange.

Title	A proteomic map of human choroid tissue
Description	The choroid is the vascular layer situated between the outer sclera and the inner retina. Together with the ciliary body and the iris it forms the uvea. Because of its rich blood supply it is also called the nutritive layer and it supplies oxygen and nutrition to the retinal pigment epithelium and the outer retina. Due to its vascular nature it acts as a heat sink and helps in thermoregulation within the eye. It also contains a pigment “melanin”, which absorbs excess light within the eye and prevents scattering. . The human choroid is thickest posteriorly where it measures 0.2 mm, whereas anteriorly it measures 0.1 mm.. The aim of this study was to characterize the choroid proteome to generate a resource for future studies on the choroid . The method used in this study combined bRPLC and LC-MS/MS analysis of the proteins isolated from the three cadaver samples of healthy donors. Subsequently, we classified the proteins based on gene ontology and pathway analysis. A total of 5,249 non redundant proteins were identified in the human choroid. Gene ontology classification pinpointed proteins involved in protein metabolism, regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism, transport, cell growth and/or maintenance and immune response. Several proteins identified in normal choroid have previously been identified in human choroid where these proteins are related to glaucoma, ocular inflammation, toxoplasmic retinochoroiditis, diabetic retinopathy, open-angle glaucoma and Grave’s disease. The top canonical pathway in which the choroid proteins participated are EIF2 signaling, integrin signalling, mitochondrial dysfunction, regulation of eIF4 and p70S6K signaling and clathrin-mediated endocytosis signalling. Around 800 choroid proteins were related to infectious diseases. The results of this study illustrate the largest number of proteins identified in human choroid and may serve as a valuable resource for future investigations of choroid biology and disease. Proteomic analysis of choroid proteins could provide versatile information to understand choroidal functions and the underlying pathogenesis of choroidal pathologies.
HostingRepository	PRIDE
AnnounceDate	2018-04-25
AnnouncementXML	Submission_2018-04-25_00:07:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	L-methionine sulfoxide; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-01 01:15:32	ID requested
⏵ 1	2018-04-25 00:07:03	announced

Dammalli M, Murthy KR, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Nair B, Gowda H, Keshava Prasad TS, Toward Postgenomics Ophthalmology: A Proteomic Map of the Human Choroid-Retinal Pigment Epithelium Tissue. OMICS, 21(2):114-122(2017) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Human, Eye, Choroid, bRPLC, LC-MS/MS,

Akhilesh Pandey
contact affiliation	McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 USA
contact email	pandey@jhmi.edu
lab head
Akhilesh Pandey
contact affiliation	Johns Hopkins University
contact email	pandey@jhmi.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/2018/04/PXD002273

PRIDE project URI

• PRIDE
  1. PXD002273
     1. Label: PRIDE project
     2. Name: A proteomic map of human choroid tissue