PXD039490

PXD039490 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of embryonic retina to facilitate ocular disease gene discovery
Description	To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend the iSyTE approach to retina development on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches–involving either transcriptomics or proteomics–pose a key challenge of prioritizing select candidates from thousands of RNA/proteins expressed in a particular cell/tissue type. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis–termed “in silico WB-subtraction”–with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of 2.5 average spectral counts, 2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information by the research community to facilitate eye gene discovery.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:05:19.702.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Phillip Wilmarth
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-16 13:51:49	ID requested
1	2023-10-09 09:17:39	announced
2	2023-10-16 07:05:43	announced	2023-10-16: Updated project metadata.
3	2023-11-14 09:06:08	announced	2023-11-14: Updated project metadata.
⏵ 4	2024-10-22 06:05:20	announced	2024-10-22: Updated project metadata.

10.1007/s00439-023-02570-0;

Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA, Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Hum Genet, 142(7):927-947(2023) [pubmed]

submitter keyword: Gene discovery, Proteome, Embryogenesis,Retina, Mass spectrometry, iSyTE, Development

Dr. Salil Lachke
contact affiliation	Department of Biological Sciences University of Delaware Newark, DE, USA.
contact email	salil@udel.edu
lab head
Phillip Wilmarth
contact affiliation	OHSU
contact email	wilmarth@ohsu.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/2023/10/PXD039490

PRIDE project URI

• PRIDE
  1. PXD039490
     1. Label: PRIDE project
     2. Name: Proteomic profiling of embryonic retina to facilitate ocular disease gene discovery