Evidence map›Paper›PMID 40728928›Full record

ArticleCell reports2025

A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space.

Luke T G Harland, Tim Lohoff, Noushin Koulena, Nico Pierson, Constantin Pape, Farhan Ameen, Jonathan Griffiths, Bart Theeuwes, Nicola K Wilson, Anna Kreshuk and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Resolving cell lineages and gene functions in the developing mouse gastrointestinal tract using in utero transduction.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  3. Review
  4. Review
  5. Article
  6. Article
  7. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Luke T G HarlandCambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wolfson College, University of Cambridge, Cambridge, UK. Electronic address: ltgh2@cam.ac.uk.
Tim LohoffEpigenetics Programme, The Babraham Institute, Cambridge, UK.
Noushin KoulenaDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Nico PiersonDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Constantin PapeInstitute of Computer Science, Georg-August University Göttingen, Göttingen, Germany.
Farhan AmeenSchool of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia; Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia; Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia.
Jonathan GriffithsCancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
Bart TheeuwesCambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK.
Nicola K WilsonCambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK.
Anna KreshukCell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Wolf ReikEpigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
Jennifer NicholsMRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK.
Long CaiDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
John C MarioniCancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
Berthold GöttgensCambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK. Electronic address: bg200@cam.ac.uk.
Shila GhazanfarSchool of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia; Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia; Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia. Electronic address: shila.ghazanfar@sydney.edu.au.

Funding

Comprehensive reference map construction, geolocation and data integration for HuBMAP HIVEOT2OD026673 · OD · NEW YORK GENOME CENTER · PI MARIONI, JOHN CARLO, SATIJA, RAHUL · 2018 to 2021
$2.9M
NIH HHS OT2 OD026673Wellcome Trust 220379Wellcome Trust 226309
6 · The paper itself

Abstract

During gastrulation, mouse epiblast cells form the three germ layers that establish the body plan and initiate organogenesis. While single-cell atlases have advanced our understanding of lineage diversification, spatial aspects of differentiation remain poorly defined. Here, we applied spatial transcriptomics to mouse embryos at embryonic (E) E7.25 and E7.5 days and integrated these data with existing E8.5 spatial and E6.5-E9.5 single-cell RNA-seq atlases. This resulted in a spatiotemporal atlas of over 150,000 cells with 82 refined cell-type annotations. The resource enables exploration of gene expression dynamics across anterior-posterior and dorsal-ventral axes, uncovering spatial logic guiding mesodermal fate decisions in the primitive streak. We also developed a computational pipeline to project additional single-cell datasets into this framework for comparative analysis. Freely accessible through an interactive web portal, this atlas offers a valuable tool for the developmental and stem cell biology communities to investigate mouse embryogenesis in a spatial and temporal context.

Indexed as

Body PatterningGastrulationOrganogenesisAnimalsEmbryo, MammalianGene Expression Regulation, DevelopmentalGerm LayersMiceSingle-Cell AnalysisSpatio-Temporal AnalysisTranscriptomeaxial patterningCP: Developmental biologyCP: Genomicsgastrulationgastruloidsmouse developmentorganogenesissingle cell transcriptomicsspatial transcriptomicsspatiotemporal atlas

Identifiers

PMID40728928
PMCPMC7618461

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

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 OpenQuestion graph.