Mouse Embryonic Lineage Atlas

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Data & archive

Per-embryo H5TD files — gene expression counts, cell metadata, and lineage trees — along with combined CSV tables are archived on Zenodo. Each box below links directly to that file for download.

Open Zenodo record ↗

H5TD files containing gene expression counts, cell meta data, and lineage trees can be loaded using TreeData and analyzed using Pycea, or visualized directly using CELLxLINEAGE. R users can load H5TD files using TreeDataR.

New to the data? The mouse embryogenesis tutorial in the Pycea documentation is a good place to start analyzing it.

Combined tables

Supplementary tables

Cite this dataset

Colgan WN, Koblan LW, Villagrana J, Hou T-CJ, Wang M, Gowri G, Chandler W, Sepulveda LA, Ciftci D, Smolyar K, Young A, Wittler L, Markoulaki S, Loh KM, Zhuang X, Yosef N, Smith ZD, Weissman JS. Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis. bioRxiv (2026). doi:10.64898/2026.05.07.722278

BibTeX 
@article{colgan2026mela,
  title   = {Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis},
  author  = {Colgan WN, Koblan LW, Villagrana J, Hou T-CJ, Wang M, Gowri G, Chandler W, Sepulveda LA, Ciftci D, Smolyar K, Young A, Wittler L, Markoulaki S, Loh KM, Zhuang X, Yosef N, Smith ZD, Weissman JS},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.64898/2026.05.07.722278},
  url     = {https://www.biorxiv.org/content/10.64898/2026.05.07.722278v2}
}