A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup Article Swipe
Chengxiang Qiu
,
Beth Martin
,
Ian Welsh
,
Riza M. Daza
,
Truc-Mai Le
,
Xingfan Huang
,
Eva K. Nichols
,
Megan L. Taylor
,
Olivia Fulton
,
Diana R. O’Day
,
Anne Roshella Gomes
,
Saskia Ilcisin
,
Sanjay Srivatsan
,
Xinxian Deng
,
Christine M. Distèche
,
William Stafford Noble
,
Nobuhiko Hamazaki
,
Cecilia B. Moens
,
David Kimelman
,
Junyue Cao
,
Alexander F. Schier
,
Malte Spielmann
,
Stephen A. Murray
,
Cole Trapnell
,
Jay Shendure
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.04.05.535726
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.04.05.535726
The house mouse, Mus musculus , is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
Related Topics
Concepts
Somitogenesis
Biology
Gastrulation
Embryonic stem cell
Fate mapping
Embryo
Cell biology
Cell type
Embryogenesis
Genetics
Cell
Computational biology
Gene
Somite
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2023.04.05.535726
- https://www.biorxiv.org/content/biorxiv/early/2023/04/05/2023.04.05.535726.full.pdf
- OA Status
- green
- Cited By
- 20
- References
- 118
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4362671298
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4362671298Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/2023.04.05.535726Digital Object Identifier
- Title
-
A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pupWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-04-05Full publication date if available
- Authors
-
Chengxiang Qiu, Beth Martin, Ian Welsh, Riza M. Daza, Truc-Mai Le, Xingfan Huang, Eva K. Nichols, Megan L. Taylor, Olivia Fulton, Diana R. O’Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M. Distèche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B. Moens, David Kimelman, Junyue Cao, Alexander F. Schier, Malte Spielmann, Stephen A. Murray, Cole Trapnell, Jay ShendureList of authors in order
- Landing page
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https://doi.org/10.1101/2023.04.05.535726Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2023/04/05/2023.04.05.535726.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2023/04/05/2023.04.05.535726.full.pdfDirect OA link when available
- Concepts
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Somitogenesis, Biology, Gastrulation, Embryonic stem cell, Fate mapping, Embryo, Cell biology, Cell type, Embryogenesis, Genetics, Cell, Computational biology, Gene, SomiteTop concepts (fields/topics) attached by OpenAlex
- Cited by
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20Total citation count in OpenAlex
- Citations by year (recent)
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2025: 4, 2024: 12, 2023: 4Per-year citation counts (last 5 years)
- References (count)
-
118Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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