A million-cell lineage tree of one mouse embryo, rooted at the zygote.

The first two are the trees themselves; the other three are analyses built on them. Every view is linkable — the bar at the top of the browser always holds a URL that encodes the current tab and all of its settings.

Both are dated in embryonic time from the zygote (E0) through two blastomeres (E1.5) to all tips at E13.5. The dating places 656 lineages at E6.5; branch lengths are continuous, and the viewer's time axis is computed from them directly.

Tips

Each profiled cell carries a cell-type call, a major-trajectory assignment and a germ-layer assignment transferred from the mouse embryo atlas of Qiu et al. 138 cell types, 25 trajectories and 6 germ layers are represented. Germ-layer assignments are lineage-validated.

Internal nodes (ancestral states)

Ancestral cell types were imputed by walking up the tree in half-day steps and matching each node to the atlas in UMAP space with a mutual-nearest-neighbour strategy. 926,852 of the 1,054,879 internal nodes within the atlas interval (88%) carry a call, with coverage lowest early (46% at E8.75) and best late (96–98% between E11.5 and E13.0).

These per-node calls are not shown in the two tree browsers. Individually they are too noisy to read one at a time, so the browsers display only what is reconstructed — topology, dating, edit patterns, and the composition of a clade's own profiled cells. The imputed layer is used only in the three analysis views, and only behind an explicit filter.

Both trees are written directly from the same artifacts this browser is built from, so their topology, dating and node numbering are identical to what you see on screen. Newick format, gzipped. Branch lengths are in days, so a node's age is the sum of branch lengths from the root: the root sits at E0.0 and every tip at E13.5 (the trees are ultrametric to within about 3.3 seconds).

Labels. Tip labels are cell_id values, the join key for the single-cell metadata. Internal labels are n<id>, where the id is the node's preorder index and matches the node numbering used by this browser — note that the full tree and the backbone tree number their nodes independently, so n1234 is not the same node in both files. These are identifiers only: the imputed ancestral cell-type calls are deliberately not included in these files, since they are model output rather than reconstruction, and are better read in context in the browser.

Loading the trees

In Python with TreeSwift, which reads the gzipped file directly (about half a minute for the full tree on a laptop):

import treeswift, pandas as pd

tree = treeswift.read_tree_newick("nextcell_full_tree_dated.nwk.gz")
age  = {n.label: d for n, d in tree.distances_from_root()}   # days since the zygote
meta = pd.read_csv("cell_metadata.v8.txt.gz", sep="\t").set_index("cell_id")
tips = meta.loc[[n.label for n in tree.traverse_leaves()]]   # one row per cell in the tree

The cell metadata file is in the code repository; see Data & code.

@article{yu2026dnatypewriter,
  title   = {A {DNA} Typewriter records the cell lineage history of a mouse,
             from zygote to late organogenesis},
  author  = {Yu, Qi and Kim, Haedong and Seidel, Sophie and Acosta-Clark, James F. and Martin, Beth K. and O'Connor, Kyle and Daza, Riza M. and Gasperini, Molly and Nathans, Jenny F. and Lam, Maggie and Gamo, Elena and VijayKumar, Shruthi and Kuo, Lauren and Lalanne, Jean-Beno{\^i}t and Simeonov, Kamen P. and Pepper, Marion and Trapnell, Cole and Gray, Jesse M. and Choi, Junhong and Qiu, Chengxiang and Shendure, Jay},
  journal = {Science},
  year    = {2026},
  doi     = {10.1126/science.ael0508}
}

Affiliations

1. Department of Genome Sciences, University of Washington, Seattle, WA, USA
2. Seattle Hub for Synthetic Biology, Seattle, WA, USA
3. Howard Hughes Medical Institute, Seattle, WA, USA
4. Allen Institute, Seattle, WA, USA
5. Medical Scientist Training Program, University of Washington, Seattle, WA, USA
6. Present address: Département de Biochimie et Médecine Moléculaire & Courtois Institute for Biomedical Innovation, Université de Montréal, Montréal, QC, Canada
7. Public Health Sciences Division / Translational Research Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
8. Department of Immunology, University of Washington, Seattle, WA, USA
9. Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
10. Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
11. Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
12. Present address: Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
13. Department of Molecular and Systems Biology, Dartmouth College, Hanover, NH, USA
14. AI BioDesign, Seattle, WA, USA

Acknowledgements

We thank the members of the Shendure lab, the Seattle Hub for Synthetic Biology, Allen Discovery Center for Cell Lineage, and UW Genome Sciences communities for helpful discussions over the course of many years (particularly the Shendure/SeaHub Recording subgroup, A. Schier, M. Elowitz, R. Waterston, and W. Colgan). We also thank the Transgenic Colony Management, Neurosurgery & Behavior, Lab Animal Services, and the Veterinary Services teams at the Allen Institute for their contributions to animal work. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. This research was supported in part by the Brotman Baty Institute for Precision Medicine, as well as the Allen Institute, founded by Jody Allen – chair and co-founder of Allen Family Philanthropies, and the late Paul G. Allen – investor, philanthropist, and co-founder of Microsoft. We gratefully acknowledge their vision and generosity, which make this work possible. J.S. is an Investigator of the Howard Hughes Medical Institute.

Funding

• Allen Institute (JS)
• Brotman Baty Institute for Precision Medicine (JS)
• Cancer Research Society of Canada grant 1155581 (J-BL)
• Chan Zuckerberg Initiative Foundation, Seattle Hub for Synthetic Biology award CZIF2023-008738 (JS, CT, MP)
• Charles H. Hood Foundation, Inc., MA (CQ)
• Damon Runyon Cancer Research Foundation grant DFS-64-24 (JC)
• Damon Runyon Cancer Research Foundation grant DRG-2435-21 (J-BL)
• Howard Hughes Medical Institute (JS)
• National Institutes of Health grant R00HG012973 (JC)
• National Institutes of Health grant P30CA008748 (JC)
• National Institutes of Health grant P20GM130454, via Dartmouth’s Center for Quantitative Biology (CQ)
• Paul G. Allen Frontiers Group, Allen Discovery Center for Cell Lineage Tracing (JS, CT)
• Searle Scholars Award SSP-2025-101 (JC)
• Swiss National Science Foundation Postdoc. Mobility fellowship grant 239394 (SS)
• Washington Research Foundation Postdoctoral Fellowship (HK)

Competing interests

The University of Washington has filed a patent application related to DNA Typewriter (US20240355418A1), on which JC and JS are listed as inventors. JS is on the scientific advisory board, a consultant, and/or a co-founder of 10x Genomics, Cellular Intelligence, Guardant Health, Pacific Biosciences and Phase Genomics. CT is a paid consultant for 10x Genomics and holds equity in the company. KPS is a member of the Translational Advisory Council at SeaBridge, Allen Institute. All other authors declare no competing interests.

AI disclosure

Several authors used AI-based tools during this work. The NextCell interactive browser was built with Claude Code (Anthropic). Data exploration, data analysis, data visualisation, and code development were additionally supported by Claude Opus 5, Claude Opus 4.7, and Claude Sonnet 5 (Anthropic), which were also used to improve the readability and language of the manuscript. AI-assisted tools were not used to generate or alter primary data, to draw scientific conclusions, or to perform other key authoring tasks. All AI-assisted code, analyses, and text were reviewed, tested, and edited by the authors, who take full responsibility for the data, code, analyses, and conclusions presented here.

On the name and the mark

This browser owes an obvious debt to Nextstrain, and the NextCell mark is an intentional homage to theirs: a disc of flat, spectrally coloured facets. The geometry is our own — where Nextstrain’s mark is a globe, ours is a radial dendrogram, one cell at the centre dividing outward, which is how Fig. 3A of the paper draws this tree. The artwork is original and NextCell is not affiliated with, endorsed by, or connected to the Nextstrain project.