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Cited by 764Single-cell and spatial transcriptomicsDevelopmental Biology and Gene RegulationGenomics and Chromatin Dynamics

A human cell atlas of fetal gene expression

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Cao, Junyue, O’Day, Diana R., Pliner, Hannah A., Kingsley, Paul D., Deng, Mei, Daza, Riza M., Zager, Michael A., Aldinger, Kimberly A. +9 more·2020·Science
DOI 10.1126/science.aba7721PMC PMC7780123
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Abstract

The genomics of human development: Understanding the trajectory of a developing human requires an understanding of how genes are regulated and expressed. Two papers now present a pooled approach using three levels of combinatorial indexing to examine the single-cell gene expression and chromatin landscapes from 15 organs in fetal samples. Cao et al. focus on measurements of RNA in broadly distributed cell types and provide insights into organ specificity. Domcke et al. examined the chromatin accessibility of cells from these organs and identify the regulatory elements that regulate gene expression. Together, these analyses generate comprehensive atlases of early human development. Science , this issue p. eaba7721 , p. eaba7612

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  • In silico deletion of TBX5 in fetal cardiomyocytes more significantly impacted its direct targets (as defined by ChIP-seq) compared to indirect targets and housekeeping genes.

    “Analogously, in silico deletion of TBX5, another known congenital heart disease gene, in fetal cardiomyocytes23 more significantly impacted its direct targets (as defined by ChIP-seq34) compared to indirect targets and housekeeping genes (Extended Data Fig. 9f).”

    From Transfer learning enables predictions in network biology (2023) · cites this paper as [23]

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Cited by

Sorted by citations

Authors
Cao, J., O’Day, D. R., Pliner, H. A., Kingsley, P. D., Deng, M., Daza, R. M., Zager, M. A., Aldinger, K. A., Blecher-Gonen, R., Zhang, F., Spielmann, M., Palis, J., Doherty, D., Steemers, F. J., Glass, I. A., Trapnell, C., & Shendure, J.
Affiliations
  • University of Washington (US)
  • Brotman Baty Institute (US)
  • University of Rochester Medicine (US)
  • Fred Hutch Cancer Center (US)
  • Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Illumina (United States) (US)
  • Max Planck Institute for Molecular Genetics (DE)
  • Howard Hughes Medical Institute (US)
Corresponding author
  • Trapnell, Cole
  • Shendure, Jay
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2020-11-13
Volume
370
Issue
6518
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.aba7721
PMC
PMC7780123
OpenAlex
W3103797259
Cited by
764
References
23
Citations by year
2026: 104 · 2025: 134 · 2024: 147 · 2023: 118 · 2022: 148 · 2021: 102 · 2020: 8 · 2019: 1 · 2013: 1
FWCI
30.82
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Funders
  • National Institutes of Health (NICHD R24HD000836)
  • Howard Hughes Medical Institute
  • NIH Office of the Director (R01 DK119285)
  • Deutsche Forschungsgemeinschaft (SP1532/3-1, SP1532/4-1, SP1532/5-1)
  • Paul G. Allen Frontiers Foundation (Allen Discovery Center grant)
  • Brotman Baty Institute for Precision Medicine
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
human fetal development, cell specification, single-cell gene expression, chromatin accessibility, fetal tissue, cell type annotation, fetal erythropoiesis, adrenal gland, endothelial cells, epithelial cells
MeSH terms
Atlases as Topic, Chromatin, Fetus, Humans, Neurons, Transcription Factors, Gene Expression Regulation, Developmental, Gene Expression Profiling, Single-Cell Analysis

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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