A proteogenomic atlas of the human neural retina.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39371417", "kind": "science-record", "revision": 3, "content_hash": "sha256:cf633fdab927e53112b704731b671a950add1b07d10a6f4805e41afb93671a4a", "created_at": "2026-11-01T20:29:34Z", "updated_at": "2026-11-01T22:12:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A proteogenomic atlas of the human neural retina.", "doi": "10.3389/fgene.2024.1451024", "pmid": "39371417", "authors": ["Tabea V Riepe", "Merel Stemerdink", "Renee Salz", "Alfredo Dueñas Rey", "Suzanne E de Bruijn", "Erica Boonen", "Tomasz Z Tomkiewicz", "Michael Kwint", "Jolein Gloerich", "Hans J C T Wessels", "Emma Delanote", "Elfride De Baere", "Filip van Nieuwerburgh", "Sarah De Keulenaer", "Barbara Ferrari", "Stefano Ferrari", "Frauke Coppieters", "Frans P M Cremers", "Erwin van Wyk", "Susanne Roosing", "Erik de Vrieze", "Peter A C 't Hoen"], "journal": "Frontiers in genetics", "year": 2024, "abstract": "The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNA-sequencing methods have been used for understanding retina-specific splicing but have limitations in detailing transcript isoforms. To address this, we generated a proteogenomic atlas that combines PacBio long-read RNA-sequencing data with mass spectrometry and whole genome sequencing data of three healthy human neural retina samples. We identified nearly 60,000 transcript isoforms, of which approximately one-third are novel. Additionally, ten novel peptides confirmed novel transcript isoforms. For instance, we identified a novel IMPDH1 isoform with a novel combination of known exons that is supported by peptide evidence. Our research underscores the potential of in-depth tissue-specific transcriptomic analysis to enhance our grasp of tissue-specific alternative splicing. The data underlying the proteogenomic atlas are available via EGA with identifier EGAD50000000101, via ProteomeXchange with identifier PXD045187, and accessible through the UCSC genome browser.", "claims": [{"id": "claim-method", "statement": "Comparison of length between novel and known isoforms was tested using a Mann-Whiney-U test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39371417", "locator": "sections[18] \"2.16 Length and TPM comparison between known and novel transcripts\" paragraph 2", "quote": "Comparison of length between novel and known isoforms was tested using a Mann-Whiney-U test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: http://www.proteomexchange.org/, PXD045187; https://ega-archive.org, EGAD50000000101. USCS genome browser tracks of the analyzed transcriptomics and proteomics data are available at https://genome-euro.ucsc.edu/s/tabeariepe/retina_atlas. All original code has been deposited at GitHub (https://github.com/cmbi/Neural-Retina-Atlas) and is publicly available as of the date of publication.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39371417", "locator": "sections[31] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: http://www.proteomexchange.org/, PXD045187; https://ega-archive.org, EGAD50000000101. USCS genome browser tracks of the analyzed transcriptomics and proteomics data are available at https://genome-euro.ucsc.edu/s/tabeariepe/retina_atlas. All original code has been deposited at GitHub (https://github.com/cmbi/Neural-Retina-Atlas) and is publicly available as of the date of publication."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Novel transcripts (NIC and NNIC) were longer than known transcripts (Mann-Whitney-U test: W = 5.78 × 108, p-value <0.05 (Supplementary Figure S1F).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Novel transcripts (NIC and NNIC) were longer than known transcripts (Mann-Whitney-U test: W = 5.78 × 108, p-value <0.05 (Supplementary Figure S1F)."}, "evidence": [{"asset": "source:pmid:39371417", "locator": "sections[25] \"3.3 Iso-Seq reveals novel neural retinal transcripts\" paragraph 2", "quote": "Novel transcripts (NIC and NNIC) were longer than known transcripts (Mann-Whitney-U test: W = 5.78 × 108, p-value <0.05 (Supplementary Figure S1F)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Novel transcripts (NIC and NNIC) were longer than known transcripts (Mann-Whitney-U test: W = 5.78 × 108, p-value <0.05 (Supplementary Figure S1F).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39371417"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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