{
  "abstract": ". Here, we use PEtracer to continuously install heritable genetic marks as cells divide, reconstructing lineage trees that resolve ~75% of cell divisions across >1.5 million cells from 16 mouse embryos collected at half-day intervals from E7.5-E10.0. We pair these trees with deep transcriptional profiling to chart the landscape of cell fate decisions during gastrulation and early organogenesis. Using these data, we quantify cell fate biases, restriction timing, progenitor pool sizes, and lineage relationships across the embryo, revealing strikingly reproducible lineage architecture across replicate embryos despite the regulative flexibility of mammalian development. We further show how lineage, spatial position, and signaling jointly determine fate outcomes and timing, with their relative influence varying by tissue. This dataset provides a quantitative framework for understanding cell fate specification and a lineage-resolved reference for generating and contextualizing developmental hypotheses at organismal scale.",
  "abstract_shown": true,
  "affiliations": [
    "Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; David H. Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA",
    "Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; David H. Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: lkoblan@wi.mit.edu",
    "Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA",
    "Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA",
    "Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA",
    "Max Planck Institute of Molecular Genetics, Max Planck Society, 14195 Berlin, Germany",
    "Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA",
    "Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel",
    "Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA; Max Planck Institute of Molecular Genetics, Max Planck Society, 14195 Berlin, Germany. Electronic address: z.smith@yale.edu",
    "Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; David H. Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: weissman@wi.mit.edu"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 19,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "William N. Colgan",
      "orcid": "0000-0002-8328-4672"
    },
    {
      "affs": [
        1
      ],
      "name": "Luke W. Koblan",
      "orcid": "0000-0003-2814-4412"
    },
    {
      "affs": [
        2
      ],
      "name": "JoAnne Villagrana",
      "orcid": "0000-0001-7023-5970"
    },
    {
      "affs": [
        2
      ],
      "name": "Tien-Chi Jason Hou",
      "orcid": "0000-0002-8349-3132"
    },
    {
      "affs": [
        2
      ],
      "name": "Minming Wang",
      "orcid": "0000-0002-5377-5518"
    },
    {
      "name": "Gokul Gowri"
    },
    {
      "affs": [
        3
      ],
      "name": "Whitney Chandler"
    },
    {
      "affs": [
        4
      ],
      "name": "Leonardo A. Sepúlveda",
      "orcid": "0000-0003-3602-1009"
    },
    {
      "affs": [
        4
      ],
      "name": "Didar Ciftci",
      "orcid": "0000-0001-8079-1022"
    },
    {
      "affs": [
        0
      ],
      "name": "Karina Smolyar"
    },
    {
      "affs": [
        0
      ],
      "name": "Kathryn E. Yost",
      "orcid": "0000-0001-6807-950X"
    },
    {
      "affs": [
        3
      ],
      "name": "Alicia Young"
    },
    {
      "affs": [
        5
      ],
      "name": "Lars Wittler",
      "orcid": "0000-0001-7873-6702"
    },
    {
      "affs": [
        3
      ],
      "name": "Styliani Markoulaki",
      "orcid": "0000-0003-4040-2365"
    },
    {
      "affs": [
        6
      ],
      "name": "Kyle M. Loh",
      "orcid": "0000-0002-8042-0149"
    },
    {
      "affs": [
        4
      ],
      "name": "Xiaowei Zhuang",
      "orcid": "0000-0002-6034-7853"
    },
    {
      "affs": [
        7
      ],
      "name": "Nir Yosef",
      "orcid": "0000-0001-9004-1225"
    },
    {
      "affs": [
        8
      ],
      "name": "Zachary D. Smith",
      "orcid": "0000-0002-9283-1957"
    },
    {
      "affs": [
        9
      ],
      "name": "Jonathan S. Weissman",
      "orcid": "0000-0003-2445-670X"
    }
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  "doi": "10.1016/j.cell.2026.09.050",
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  "published": "2026-10-01",
  "publisher": "Cell Press",
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  "title": "Comprehensive lineage tracing maps the landscape of cell fate decisions in mouse embryogenesis",
  "title_text": "Comprehensive lineage tracing maps the landscape of cell fate decisions in mouse embryogenesis",
  "type": "peer-reviewed",
  "updated_at": "2026-11-06T13:20:30Z",
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