PXD045187

PXD045187 is an original dataset announced via ProteomeXchange.

Title	A proteogenomic atlas of the human neural retina
Description	The human neural retina is enriched for alternative splicing, and it is estimated that more than 10% of variants associated with inherited retinal diseases (IRDs) alter splicing. Previous research mainly used short-read RNA-sequencing techniques to investigate retina-specific splicing and splicing factors. However, this technique provides limited information about transcript isoforms. To gain a deeper understanding of the human neural retina and its isoforms, we generated a proteogenomic atlas that combined PacBio long-read RNA-sequencing data with mass-spectrometry and whole-genome sequencing data from three healthy human neural retina samples. RNA-sequencing revealed that one-third of all transcripts were novel, and for IRD-associated genes, even 43% were novel. The most common novel elements of these transcripts were alternative poly(A) sites, exon elongation, and intron retention. Some novel elements affect the non-coding region but for more than 50% of the novel transcripts a novel open reading frame was predicted. Using proteomics, ten novel peptides confirmed novel isoforms in five genes. Additionally, we found novel isoforms of IMPDH1, an IRD-associated gene, with supporting peptide evidence. This study provides a comprehensive overview of the transcript and protein isoforms expressed in the healthy human neural retina. Moreover, it highlights the importance of studying tissue specific transcriptomes in greater detail to better understand tissue-specific regulation and to identify disease-causing variants.
HostingRepository	PRIDE
AnnounceDate	2024-10-17
AnnouncementXML	Submission_2024-10-17_02:46:41.469.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tabea Riepe
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-07 03:26:38	ID requested
⏵ 1	2024-10-17 02:46:42	announced

10.3389/fgene.2024.1451024;

Riepe TV, Stemerdink M, Salz R, Rey AD, de Bruijn SE, Boonen E, Tomkiewicz TZ, Kwint M, Gloerich J, Wessels HJCT, Delanote E, De Baere E, van Nieuwerburgh F, De Keulenaer S, Ferrari B, Ferrari S, Coppieters F, Cremers FPM, van Wyk E, Roosing S, de Vrieze E, 't Hoen PAC, A proteogenomic atlas of the human neural retina. Front Genet, 15():1451024(2024) [pubmed]

submitter keyword: Human, PacBio long-read RNA-sequencing, proteogenomics, neural retina, MSFragger, dda-PASEF

Peter-Bram 't Hoen
contact affiliation	Department of Medical BioSciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.
contact email	Peter-Bram.tHoen@radboudumc.nl
lab head
Tabea Riepe
contact affiliation	Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands.
contact email	tabea.riepe@radboudumc.nl
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/2024/10/PXD045187

PRIDE project URI

• PRIDE
  1. PXD045187
     1. Label: PRIDE project
     2. Name: A proteogenomic atlas of the human neural retina