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PXD045187-1

PXD045187 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA proteogenomic atlas of the human neural retina
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-17
AnnouncementXMLSubmission_2024-10-17_02:46:41.469.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTabea Riepe
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListacetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumenttimsTOF Pro 2
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-09-07 03:26:38ID requested
12024-10-17 02:46:42announced
Publication List
10.3389/fgene.2024.1451024;
Keyword List
submitter keyword: Human, PacBio long-read RNA-sequencing, proteogenomics, neural retina, MSFragger, dda-PASEF
Contact List
Peter-Bram 't Hoen
contact affiliationDepartment of Medical BioSciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.
contact emailPeter-Bram.tHoen@radboudumc.nl
lab head
Tabea Riepe
contact affiliationDepartment of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands.
contact emailtabea.riepe@radboudumc.nl
dataset submitter
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Dataset FTP location
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