{
  "abstract": "Short-read sequencing-based single-cell transcriptomics represents the current gold standard for studying cellular transcriptomes but remains limited in its ability to resolve full-length transcript isoforms and splicing patterns. Long-read single-cell and single-nucleus RNA sequencing (LR sc/snRNA-seq) enables the transcriptome-wide characterization of full-length isoforms at cellular resolution, yet the relative performance of commercially available workflows remains insufficiently explored. Here, using nuclei extracted from a standardized multi-species benchmark sample and Oxford Nanopore Technologies long-read sequencing, we systematically benchmarked four LR snRNA-seq strategies: 10x Genomics 3', 10x Genomics 5', ArgenTag, and Parse Biosciences. Comparing transcriptome features qualitatively and quantitatively, as well as the concordance with matched short-read data and the ability to resolve cellular heterogeneity, we identified substantial method-specific differences in read length and yield, transcript coverage, isoform detection, and recovery of sample-specific biological information, with the 10x Genomics 3' and 5' assays emerging as the most balanced approaches for comprehensive isoform-resolved single-nucleus transcriptomics. Altogether, our study provides a systematic assessment of four commercially available workflows for performing LR snRNA-seq and highlights key methodological trade-offs related to distinct library preparation strategies, thus providing practical guidance for future isoform-resolved transcriptome studies at the single-nucleus level.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "name": "F. Köhler"
    },
    {
      "name": "A. Delgado-Tejedor"
    },
    {
      "name": "M. Zehnsdorf"
    },
    {
      "name": "M. Salgado Albarran"
    },
    {
      "name": "L. Zalba Jadraque"
    },
    {
      "name": "I. Gonzalez Navarrete"
    },
    {
      "name": "L. Cozzuto"
    },
    {
      "name": "J. Ponomarenko"
    },
    {
      "name": "B. Fuste Perez"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6hab6p1qefe8e.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.01.748518",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748518v1.full",
  "id": "6hab6p1qefe8e",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748518v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7208832156",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748518v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6hab6p1qefe8e.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:33Z",
      "native_id": "10.64898/2026.09.01.748518",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748518v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Systematic benchmarking of commercial workflows for isoform-resolved single-nucleus transcriptomics",
  "title_text": "Systematic benchmarking of commercial workflows for isoform-resolved single-nucleus transcriptomics",
  "type": "preprint",
  "updated_at": "2026-10-30T12:19:33Z",
  "url": "https://research.draconitic.com/paper/6hab6p1qefe8e",
  "venue": "bioRxiv",
  "versions": []
}