{
  "abstract": "A cell's fate is shaped by its inherited state, or lineage, and the ever-shifting context of its environment. CRISPR-based recording technologies are a promising solution for mapping the lineage of a developing system; however, challenges remain regarding single-cell recovery, engineering complexity, and scale. Here, we introduce BASELINE, which uses base editing to generate high-resolution lineage trees in conjunction with single-cell profiling. BASELINE uses the Cas12a adenine base editor to irreversibly edit nucleotides across target arrays built from 50 synthetic target sites, which are integrated multiple times into a cell's genome. We demonstrate that BASELINE accumulates lineage-specific marks over a wide range of biologically relevant intervals, recording more than 4300 bits of information in a model of pancreatic cancer, a 50-fold increase over existing technologies. Single-cell sequencing reveals high-fidelity capture of these recorders, averaging 29 cell divisions captured per lineage, within the estimated range of mammalian development. We expect BASELINE to apply to a wide range of lineage-tracing projects in development and disease, especially those in which cellular engineering makes small, more distributed systems challenging.",
  "abstract_shown": true,
  "affiliations": [
    "Molecular and Cellular Biology Program, Dartmouth College , Hanover, NH, 03756 ,",
    "Molecular and Systems Biology, Dartmouth College , Hanover, NH, 03755 ,",
    "Molecular and Cellular Biology Program, Dartmouth College",
    "Quantitative Biomedical Science Program, Dartmouth College , Lebanon, NH, 03756 ,",
    "Quantititaive Biomedical Science Program",
    "POWERED Program, Dartmouth Cancer Center, Dartmouth College , Lebanon, NH, 03756 ,",
    "POWERED Program, Dartmouth College",
    "Dartmouth Cancer Center, Dartmouth College , Lebanon, NH, 03755 ,",
    "Molecular and Systems Biology, Dartmouth College"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Evan Winter"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Francesco E. Emiliani",
      "orcid": "0000-0001-6476-5166"
    },
    {
      "affs": [
        1,
        3,
        4
      ],
      "name": "Aidan Cook"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Asma Abderrahim"
    },
    {
      "affs": [
        7,
        1,
        8
      ],
      "name": "Aaron McKenna",
      "orcid": "0000-0001-8277-6512"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2kk81b2bhztha.bib",
  "cited_by": 10,
  "doi": "10.1093/nar/gkag769",
  "fulltext_url": null,
  "id": "2kk81b2bhztha",
  "issns": [
    "0305-1048",
    "1362-4954",
    "1362-4962"
  ],
  "landing_url": "https://doi.org/10.1093/nar/gkag769",
  "language": "en",
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|CRISPR and Genetic Engineering"
    ]
  ],
  "openalex": "W4408741711",
  "pdf_url": null,
  "pmcid": "PMC11957144",
  "pmid": "40166145",
  "published": "2026-07-17",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/2kk81b2bhztha.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:48Z",
      "native_id": "W4408741711",
      "source": "openalex",
      "url": "https://doi.org/10.1093/nar/gkag769"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|CRISPR and Genetic Engineering",
      "subfield": "molecular-biology"
    }
  ],
  "title": "BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing",
  "title_text": "BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T13:20:43Z",
  "url": "https://research.draconitic.com/paper/2kk81b2bhztha",
  "venue": "Nucleic Acids Research",
  "versions": []
}