PXD045187 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-09-07 03:26:38 | ID requested | |
⏵ 1 | 2024-10-17 02:46:42 | announced | |
Publication List
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] |
Keyword List
submitter keyword: Human, PacBio long-read RNA-sequencing, proteogenomics, neural retina, MSFragger, dda-PASEF |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD045187
- Label: PRIDE project
- Name: A proteogenomic atlas of the human neural retina