ArticleDevelopment (Cambridge, England)2024
Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale.
Article in Development (Cambridge, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
- Article
- A panel of Diversity Outbred mouse embryonic stem cells: enabling the functional characterization of natural genetic variationbioRxiv : the preprint server for biology · 2026Article
- Gestational exposure to PMJournal of advanced research · 2026Article
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- AXIN1 and AXIN2 regulate the WNT-signaling landscape to promote distinct mesoderm programs.Developmental cell · 2026Article
- Mosaic gastruloids reveal a temporal restriction for developmental cell competition.Nature cell biology · 2026Article
- Single-cell transcriptomic dissection of two waves of endothelial-hematopoietic transition in a murine yolk sac.Blood science (Baltimore, Md.) · 2025Article
- Modeling post-gastrula development via bidirectional pluripotent stem cells.Cell research · 2025Article
- Distinct roles of Atf3, Zfp711 and Bcl6b in early embryonic hematopoietic and endothelial lineage specification.Development (Cambridge, England) · 2025Article
- Eomes directs the formation of spatially and functionally diverse extraembryonic hematovascular tissues.Developmental cell · 2025Article
- Insights, opportunities, and challenges provided by large cell atlases.Genome biology · 2025Review
- Fibroblast growth factor 8: Multifaceted role in development and developmental disorder.Genes & diseases · 2025Review
- A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space.Cell reports · 2025Article
- A single-cell and tissue-scale analysis suite resolves Mixl1's role in heart development.iScience · 2025Article
- STAT3 signaling enhances tissue expansion during postimplantation mouse development.Cell reports · 2025Article
- In preprints: unfolding the spatial genomics frontier of mouse gastrulation.Development (Cambridge, England) · 2025Article
- Building and analyzing metacells in single-cell genomics data.Molecular systems biology · 2024Review
- Yolk sac cell atlas reveals multiorgan functions during human early development.Science (New York, N.Y.) · 2023Article
- An atlas of rabbit development as a model for single-cell comparative genomics.Nature cell biology · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
13 authors at 8 institutions in 6 countries.
Funding
Abstract
Early organogenesis represents a key step in animal development, during which pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-h intervals and combined this new dataset with our previous atlas (E6.5-E8.5) to produce a densely sampled timecourse of >400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction identified complex waves of blood and endothelial development, including a new programme for somite-derived endothelium. We also dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-seq and predicted cell fates computationally. Finally, we defined developmental state/fate relationships by combining orthotopic grafting, microscopic analysis and scRNA-seq to transcriptionally determine cell fates of grafted primitive streak regions after 24 h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with computationally predicted fates, demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in developmental biology and guide the in vitro production of cells for organ regeneration and repair.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.