A human cell atlas of fetal gene expression

The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing...

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Published in:	Science (American Association for the Advancement of Science) Vol. 370; no. 6518
Main Authors:	Cao, Junyue, O'Day, Diana R, Pliner, Hannah A, Kingsley, Paul D, Deng, Mei, Daza, Riza M, Zager, Michael A, Aldinger, Kimberly A, Blecher-Gonen, Ronnie, Zhang, Fan, Spielmann, Malte, Palis, James, Doherty, Dan, Steemers, Frank J, Glass, Ian A, Trapnell, Cole, Shendure, Jay
Format:	Journal Article
Language:	English
Published:	United States 13.11.2020
Subjects:	Atlases as Topic Chromatin - metabolism Fetus - cytology Fetus - metabolism Gene Expression Profiling Gene Expression Regulation, Developmental Humans Neurons - metabolism Single-Cell Analysis Transcription Factors - metabolism
ISSN:	1095-9203, 1095-9203
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Abstract	The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.
AbstractList	The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types. The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.
Author	Aldinger, Kimberly A Kingsley, Paul D Shendure, Jay Pliner, Hannah A Palis, James Blecher-Gonen, Ronnie Cao, Junyue Steemers, Frank J Daza, Riza M Zager, Michael A Zhang, Fan Doherty, Dan Deng, Mei O'Day, Diana R Spielmann, Malte Trapnell, Cole Glass, Ian A
Author_xml	– sequence: 1 givenname: Junyue orcidid: 0000-0003-4097-489X surname: Cao fullname: Cao, Junyue organization: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA – sequence: 2 givenname: Diana R orcidid: 0000-0002-8398-8389 surname: O'Day fullname: O'Day, Diana R organization: Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA – sequence: 3 givenname: Hannah A orcidid: 0000-0003-1484-6501 surname: Pliner fullname: Pliner, Hannah A organization: Brotman Baty Institute for Precision Medicine, Seattle, WA, USA – sequence: 4 givenname: Paul D orcidid: 0000-0003-3997-7436 surname: Kingsley fullname: Kingsley, Paul D organization: Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA – sequence: 5 givenname: Mei orcidid: 0000-0003-0480-5730 surname: Deng fullname: Deng, Mei organization: Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA – sequence: 6 givenname: Riza M orcidid: 0000-0003-1635-8675 surname: Daza fullname: Daza, Riza M organization: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA – sequence: 7 givenname: Michael A orcidid: 0000-0002-9416-8685 surname: Zager fullname: Zager, Michael A organization: Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA – sequence: 8 givenname: Kimberly A orcidid: 0000-0002-5406-8911 surname: Aldinger fullname: Aldinger, Kimberly A organization: Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA – sequence: 9 givenname: Ronnie orcidid: 0000-0003-2847-1149 surname: Blecher-Gonen fullname: Blecher-Gonen, Ronnie organization: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA – sequence: 10 givenname: Fan orcidid: 0000-0003-4340-3435 surname: Zhang fullname: Zhang, Fan organization: Illumina Inc., San Diego, CA, USA – sequence: 11 givenname: Malte orcidid: 0000-0002-0583-4683 surname: Spielmann fullname: Spielmann, Malte organization: Institute of Human Genetics, University of Lübeck, Lübeck, Germany – sequence: 12 givenname: James orcidid: 0000-0001-7324-1049 surname: Palis fullname: Palis, James organization: Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA – sequence: 13 givenname: Dan orcidid: 0000-0001-9377-028X surname: Doherty fullname: Doherty, Dan organization: Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA – sequence: 14 givenname: Frank J surname: Steemers fullname: Steemers, Frank J organization: Illumina Inc., San Diego, CA, USA – sequence: 15 givenname: Ian A orcidid: 0000-0001-6762-8407 surname: Glass fullname: Glass, Ian A organization: Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA – sequence: 16 givenname: Cole orcidid: 0000-0002-8105-4347 surname: Trapnell fullname: Trapnell, Cole email: coletrap@uw.edu, shendure@uw.edu organization: Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA – sequence: 17 givenname: Jay orcidid: 0000-0002-1516-1865 surname: Shendure fullname: Shendure, Jay email: coletrap@uw.edu, shendure@uw.edu organization: Howard Hughes Medical Institute, Seattle, WA, USA
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/33184181$$D View this record in MEDLINE/PubMed
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References	33500582 - Nature. 2021 Feb;590(7844):43-44
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Snippet	The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and...
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SubjectTerms	Atlases as Topic Chromatin - metabolism Fetus - cytology Fetus - metabolism Gene Expression Profiling Gene Expression Regulation, Developmental Humans Neurons - metabolism Single-Cell Analysis Transcription Factors - metabolism
Title	A human cell atlas of fetal gene expression
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