{
  "abstract": "Spatial transcriptomics has transformed our understanding of tissue organization, yet current high-throughput approaches remain largely confined to a gene-centric paradigm, precluding systematic characterization of spatially resolved transcript isoform diversity. Here, we introduce imaging-based spatial isoform transcriptomics (iSiT), a framework enabling simultaneous large-scale gene expression and targeted transcript isoform profiling on the commercial Xenium platform. iSiT resolves alternative splicing events that alter internal transcript structure at cellular and subcellular resolution using a single junction-specific probe per target. To facilitate broader adoption, we developed ProbeHarbour, an open-source toolkit for the design, characterization and management of isoform-specific probes. We demonstrate iSiT in the postnatal mouse brain by combining the Prime 5K gene-level panel with isoform-specific detection of 45 synaptogenesis-associated genes. By extending spatial transcriptomics beyond gene-level measurements, iSiT provides a scalable and readily accessible framework for investigating spatial isoform regulation in development and disease.",
  "abstract_shown": true,
  "affiliations": [
    "Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), CNRS UMR7275, Inserm U1323, Sophia-Antipolis, France"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "name": "E. McAndrew"
    },
    {
      "name": "M. Fierville"
    },
    {
      "name": "M. Gautier-Isola"
    },
    {
      "name": "M. Pignol"
    },
    {
      "name": "M.-J. Arguel"
    },
    {
      "name": "H. Cadis"
    },
    {
      "name": "R. Barres"
    },
    {
      "name": "B. Mari"
    },
    {
      "name": "P. BARBRY"
    },
    {
      "affs": [
        0
      ],
      "name": "K. Lebrigand"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2ckmc4d8cdgs0.bib",
  "cited_by": 1,
  "doi": "10.64898/2026.09.22.753429",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.22.753429v1.full",
  "id": "2ckmc4d8cdgs0",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.22.753429v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "neuroscience"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7214623685",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.22.753429v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-22",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/2ckmc4d8cdgs0.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:53Z",
      "native_id": "10.64898/2026.09.22.753429",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.22.753429v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:neuroscience",
      "subfield": "neuroscience"
    }
  ],
  "title": "Imaging-based spatial isoform transcriptomics resolves transcript diversity at cellular and subcellular resolution",
  "title_text": "Imaging-based spatial isoform transcriptomics resolves transcript diversity at cellular and subcellular resolution",
  "type": "preprint",
  "updated_at": "2026-10-30T12:24:53Z",
  "url": "https://research.draconitic.com/paper/2ckmc4d8cdgs0",
  "venue": "bioRxiv",
  "versions": []
}