Download
Data & archive
Per-embryo H5TD files — gene expression counts, cell metadata, and lineage trees — are archived on Zenodo. Each box below links directly to that embryo's 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.
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E7.5 · R1
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E7.5 · R2
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E7.5 · R3
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E8.0 · R1
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E8.0 · R2
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E8.0 · R3
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E8.5 · R1
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E8.5 · R2
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E8.5 · R3
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E9.0 · R1
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E9.0 · R2
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E9.0 · R3
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E9.5 · R1
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E9.5 · R2
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E9.5 · R3
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E10.0 · R1
Gene programs
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Gene program annotations
All 70 programs — genes, size, active cell types, name, and description (Table S5).
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}
}