{
  "abstract": "Linking cellular phenotype to genotype and gene expression is a central goal in biomedical research. Live-cell imaging captures dynamic cellular phenotypes, whereas single-cell sequencing measures genome-wide molecular states, but pairing these readouts for the same cell remains challenging. Here we present Waldo, a genetically encoded single-cell barcoding strategy that can be read out by both live-cell imaging and single-cell sequencing to connect single cells across both modalities. Waldo barcodes are generated by combinatorial expression of synthetic cell-surface receptors, each detected by a cognate peptide probe coupled either to a fluorescent dye or a DNA barcode. Iterative fluorescent probe staining achieves large barcode diversity, while preserving fluorescence channels for phenotypic reporters. As a proof-of-principle, we use Waldo to link cell division phenotypes after chromosome missegregation to the karyotype and transcriptome of the same cells. Waldo provides a general strategy for connecting imaging phenotypes to genome-wide sequencing readouts in single cells.",
  "abstract_shown": true,
  "affiliations": [
    "Hubrecht Institute KNAW, Oncode Institute, and University Medical Center Utrecht. 3584 CX Utrecht, The Netherlands"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 13,
  "authors": [
    {
      "name": "M. Muller"
    },
    {
      "name": "S. J. A. Lochs"
    },
    {
      "name": "L. Apperloo"
    },
    {
      "name": "R. Banerjee"
    },
    {
      "name": "J. R. Fernandes Marques"
    },
    {
      "name": "C. Davo-Martinez"
    },
    {
      "name": "P. M. J. Rullens"
    },
    {
      "name": "M. Moreno-Gonzalez"
    },
    {
      "name": "V. Papageorgiou"
    },
    {
      "name": "B. A. Kramer"
    },
    {
      "name": "G. J. Kops"
    },
    {
      "name": "J. Kind"
    },
    {
      "affs": [
        0
      ],
      "name": "M. E. Tanenbaum"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/0xke3dk5xmh6n.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.07.757257",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.07.757257v1.full",
  "id": "0xke3dk5xmh6n",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.07.757257v1",
  "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",
      "cell biology"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7221032338",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.07.757257v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-07",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/0xke3dk5xmh6n.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:26:34Z",
      "native_id": "10.64898/2026.10.07.757257",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.07.757257v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:cell biology",
      "subfield": "cell-biology"
    }
  ],
  "title": "Linking live-cell imaging to single-cell sequencing using genetic barcoding",
  "title_text": "Linking live-cell imaging to single-cell sequencing using genetic barcoding",
  "type": "preprint",
  "updated_at": "2026-10-30T12:26:34Z",
  "url": "https://research.draconitic.com/paper/0xke3dk5xmh6n",
  "venue": "bioRxiv",
  "versions": []
}