{
  "abstract": "Cell-resolved transcript structures are essential for understanding how isoform usage, alternative polyadenylation, and allelic expression vary across cell types. However, existing single-cell long-read datasets remain fragmented across studies, platforms, species, and workflows, hindering comparison and reuse. Here, we present scTHREAD (single-cell Transcriptome Hub for Long-Read Evidence, Annotation, and Discovery; https://scthread.ai4sc.ac.cn/), an open-access database for integrating, exploring, and retrieving single-cell long-read transcriptomic evidence. It comprises 453 runs from 34 human and mouse datasets, covering 923 389 cells profiled by Oxford Nanopore and PacBio. A uniform, platform-aware workflow catalogues 12 471 531 run–transcript observations, of which 30% carry one of 210 341 distinct Ensembl transcript identifiers. Isoform and poly(A)-site usage, splice-junction support, and allele-aware counts remain linked to their source study, run, cell type, and single cell, ensuring full provenance, and differential usage is precomputed where coverage permits. Records are explored through a web interface and retrieved through bulk downloads or a documented API. scTHREAD recapitulates known cell-type-specific isoform patterns and identifies reproducible monocyte–T-cell differences in CCND3, CUTA, and PSMB8 junction usage across three cohorts and two sequencing technologies, establishing it as a traceable resource for investigating RNA processing and transcript regulation at isoform resolution.",
  "abstract_shown": true,
  "affiliations": [
    "Beijing Life Science Academy, Key Laboratory of Biosynthesis and Biomanufacturing in Model Plants, Ministry of Industry and Information Technology, and GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University , Guangzhou 511436 ,",
    "Zhongshan Hospital, Fudan University , Shanghai 200032 ,",
    "State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University , Jinan 250012 ,",
    "Guangzhou National Laboratory, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University , Guangzhou 511436 ,",
    "Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University , Beijing 100193 ,",
    "Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an Jiaotong University , Xi’an 710061 ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Zhi-Can Fu"
    },
    {
      "affs": [
        2
      ],
      "name": "Yelian Yan"
    },
    {
      "affs": [
        3
      ],
      "name": "Chunchun Wu"
    },
    {
      "affs": [
        0
      ],
      "name": "Ran Song"
    },
    {
      "affs": [
        0
      ],
      "name": "Xiaobo Wang"
    },
    {
      "affs": [
        0
      ],
      "name": "Jianfan Wei"
    },
    {
      "affs": [
        4
      ],
      "name": "Zhuangzhuang Lu"
    },
    {
      "affs": [
        0
      ],
      "name": "Tietuo Tao"
    },
    {
      "affs": [
        0
      ],
      "name": "Peng Lu"
    },
    {
      "affs": [
        0
      ],
      "name": "Wentao Cui"
    },
    {
      "affs": [
        5
      ],
      "name": "Yanqiang Li"
    },
    {
      "affs": [
        2
      ],
      "name": "Keliang Wu"
    },
    {
      "affs": [
        0
      ],
      "name": "Yong Chen"
    },
    {
      "affs": [
        2
      ],
      "name": "Tao Huang"
    },
    {
      "affs": [
        0,
        3
      ],
      "name": "Shenli Yuan",
      "orcid": "0009-0009-7137-8098"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/apcce6a242j5f.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag1038",
  "fulltext_url": null,
  "id": "apcce6a242j5f",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1038/8986426",
  "language": null,
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7223357521",
  "pdf_url": "https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkag1038/72410171/gkag1038.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-23",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/apcce6a242j5f.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:50Z",
      "native_id": "10.1093/nar/gkag1038",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1038/8986426"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "scTHREAD: a cell-resolved long-read transcriptome database with linked isoform, poly(A), junction, and allelic evidence",
  "title_text": "scTHREAD: a cell-resolved long-read transcriptome database with linked isoform, poly(A), junction, and allelic evidence",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:50Z",
  "url": "https://research.draconitic.com/paper/apcce6a242j5f",
  "venue": "Nucleic Acids Research",
  "versions": []
}