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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| Veröffentlicht in: | Science (American Association for the Advancement of Science) 2020-11, Vol.370 (6518) |
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| creator | 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 |
| description | 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. |
| doi_str_mv | 10.1126/science.aba7721 |
| format | Article |
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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.</description><identifier>ISSN: 0036-8075</identifier><identifier>EISSN: 1095-9203</identifier><identifier>DOI: 10.1126/science.aba7721</identifier><identifier>PMID: 33184181</identifier><language>eng</language><publisher>United States: The American Association for the Advancement of Science</publisher><subject>Accessibility ; Adrenal glands ; Atlases as Topic ; Blood cells ; Cell differentiation ; Cell lines ; Chromatin ; Chromatin - metabolism ; Combinatorial analysis ; Data integration ; Developmental stages ; Embryogenesis ; Epigenetics ; Epithelial cells ; Erythropoiesis ; Fetus - cytology ; Fetus - metabolism ; Fetuses ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genetics ; Hematopoietic stem cells ; Heterogeneity ; Human tissues ; Humans ; In vivo methods and tests ; Indexing ; Integration ; Neurons - metabolism ; Organs ; Proteomics ; Regulatory sequences ; Ribonucleic acid ; RNA ; Single-Cell Analysis ; Specifications ; Stem cell transplantation ; Stem cells ; Tissue analysis ; Tissues ; Transcription Factors - metabolism ; Websites</subject><ispartof>Science (American Association for the Advancement of Science), 2020-11, Vol.370 (6518)</ispartof><rights>Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.</rights><rights>Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c533t-e219db0353c9613868d28626440d5040cdf16920cc935b6fbcc0c77a79fcb9343</citedby><cites>FETCH-LOGICAL-c533t-e219db0353c9613868d28626440d5040cdf16920cc935b6fbcc0c77a79fcb9343</cites><orcidid>0000-0003-2847-1149 ; 0000-0002-8398-8389 ; 0000-0003-1635-8675 ; 0000-0003-3997-7436 ; 0000-0002-9416-8685 ; 0000-0003-4340-3435 ; 0000-0003-0480-5730 ; 0000-0001-9377-028X ; 0000-0003-4097-489X ; 0000-0001-7324-1049 ; 0000-0002-1516-1865 ; 0000-0002-5406-8911 ; 0000-0001-6762-8407 ; 0000-0003-1484-6501 ; 0000-0002-8105-4347 ; 0000-0002-0583-4683</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,2871,2872,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33184181$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Cao, Junyue</creatorcontrib><creatorcontrib>O'Day, Diana R</creatorcontrib><creatorcontrib>Pliner, Hannah A</creatorcontrib><creatorcontrib>Kingsley, Paul D</creatorcontrib><creatorcontrib>Deng, Mei</creatorcontrib><creatorcontrib>Daza, Riza M</creatorcontrib><creatorcontrib>Zager, Michael A</creatorcontrib><creatorcontrib>Aldinger, Kimberly A</creatorcontrib><creatorcontrib>Blecher-Gonen, Ronnie</creatorcontrib><creatorcontrib>Zhang, Fan</creatorcontrib><creatorcontrib>Spielmann, Malte</creatorcontrib><creatorcontrib>Palis, James</creatorcontrib><creatorcontrib>Doherty, Dan</creatorcontrib><creatorcontrib>Steemers, Frank J</creatorcontrib><creatorcontrib>Glass, Ian A</creatorcontrib><creatorcontrib>Trapnell, Cole</creatorcontrib><creatorcontrib>Shendure, Jay</creatorcontrib><title>A human cell atlas of fetal gene expression</title><title>Science (American Association for the Advancement of Science)</title><addtitle>Science</addtitle><description>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.</description><subject>Accessibility</subject><subject>Adrenal glands</subject><subject>Atlases as Topic</subject><subject>Blood cells</subject><subject>Cell differentiation</subject><subject>Cell lines</subject><subject>Chromatin</subject><subject>Chromatin - metabolism</subject><subject>Combinatorial analysis</subject><subject>Data integration</subject><subject>Developmental stages</subject><subject>Embryogenesis</subject><subject>Epigenetics</subject><subject>Epithelial cells</subject><subject>Erythropoiesis</subject><subject>Fetus - cytology</subject><subject>Fetus - metabolism</subject><subject>Fetuses</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Genetics</subject><subject>Hematopoietic stem cells</subject><subject>Heterogeneity</subject><subject>Human tissues</subject><subject>Humans</subject><subject>In vivo methods and tests</subject><subject>Indexing</subject><subject>Integration</subject><subject>Neurons - metabolism</subject><subject>Organs</subject><subject>Proteomics</subject><subject>Regulatory sequences</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Single-Cell Analysis</subject><subject>Specifications</subject><subject>Stem cell transplantation</subject><subject>Stem cells</subject><subject>Tissue analysis</subject><subject>Tissues</subject><subject>Transcription Factors - metabolism</subject><subject>Websites</subject><issn>0036-8075</issn><issn>1095-9203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdkc1Lw0AQxRdRbK2evUnAiyBpZ3eS3exFKMUvKHjR87LZbNqUJFuzieh_b0pjUU9zeL95zJtHyCWFKaWMz7wpbG3sVKdaCEaPyJiCjEPJAI_JGAB5mICIR-TM-w1Ar0k8JSNEmkQ0oWNyOw_WXaXrwNiyDHRbah-4PMhtq8tgZWsb2M9tY70vXH1OTnJdensxzAl5e7h_XTyFy5fH58V8GZoYsQ0tozJLAWM0klNMeJKxhDMeRZDFEIHJcsr7C42RGKc8T40BI4QWMjepxAgn5G7vu-3SymbG1m2jS7Vtiko3X8rpQv1V6mKtVu5DCZEAZdgb3AwGjXvvrG9VVfhdQF1b13nFIg5CgMCkR6__oRvXNXUfb6CQc9lTsz1lGud9Y_PDMRTUrgg1FKGGIvqNq98ZDvzP5_EbjQyErQ</recordid><startdate>20201113</startdate><enddate>20201113</enddate><creator>Cao, Junyue</creator><creator>O'Day, Diana R</creator><creator>Pliner, Hannah A</creator><creator>Kingsley, Paul D</creator><creator>Deng, Mei</creator><creator>Daza, Riza M</creator><creator>Zager, Michael A</creator><creator>Aldinger, Kimberly A</creator><creator>Blecher-Gonen, Ronnie</creator><creator>Zhang, Fan</creator><creator>Spielmann, Malte</creator><creator>Palis, James</creator><creator>Doherty, Dan</creator><creator>Steemers, Frank J</creator><creator>Glass, Ian A</creator><creator>Trapnell, Cole</creator><creator>Shendure, Jay</creator><general>The American Association for the Advancement of Science</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QQ</scope><scope>7QR</scope><scope>7SC</scope><scope>7SE</scope><scope>7SN</scope><scope>7SP</scope><scope>7SR</scope><scope>7SS</scope><scope>7T7</scope><scope>7TA</scope><scope>7TB</scope><scope>7TK</scope><scope>7TM</scope><scope>7U5</scope><scope>7U9</scope><scope>8BQ</scope><scope>8FD</scope><scope>C1K</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-2847-1149</orcidid><orcidid>https://orcid.org/0000-0002-8398-8389</orcidid><orcidid>https://orcid.org/0000-0003-1635-8675</orcidid><orcidid>https://orcid.org/0000-0003-3997-7436</orcidid><orcidid>https://orcid.org/0000-0002-9416-8685</orcidid><orcidid>https://orcid.org/0000-0003-4340-3435</orcidid><orcidid>https://orcid.org/0000-0003-0480-5730</orcidid><orcidid>https://orcid.org/0000-0001-9377-028X</orcidid><orcidid>https://orcid.org/0000-0003-4097-489X</orcidid><orcidid>https://orcid.org/0000-0001-7324-1049</orcidid><orcidid>https://orcid.org/0000-0002-1516-1865</orcidid><orcidid>https://orcid.org/0000-0002-5406-8911</orcidid><orcidid>https://orcid.org/0000-0001-6762-8407</orcidid><orcidid>https://orcid.org/0000-0003-1484-6501</orcidid><orcidid>https://orcid.org/0000-0002-8105-4347</orcidid><orcidid>https://orcid.org/0000-0002-0583-4683</orcidid></search><sort><creationdate>20201113</creationdate><title>A human cell atlas of fetal gene expression</title><author>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</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c533t-e219db0353c9613868d28626440d5040cdf16920cc935b6fbcc0c77a79fcb9343</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Accessibility</topic><topic>Adrenal glands</topic><topic>Atlases as Topic</topic><topic>Blood cells</topic><topic>Cell differentiation</topic><topic>Cell lines</topic><topic>Chromatin</topic><topic>Chromatin - metabolism</topic><topic>Combinatorial analysis</topic><topic>Data integration</topic><topic>Developmental stages</topic><topic>Embryogenesis</topic><topic>Epigenetics</topic><topic>Epithelial cells</topic><topic>Erythropoiesis</topic><topic>Fetus - cytology</topic><topic>Fetus - metabolism</topic><topic>Fetuses</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Developmental</topic><topic>Genetics</topic><topic>Hematopoietic stem cells</topic><topic>Heterogeneity</topic><topic>Human tissues</topic><topic>Humans</topic><topic>In vivo methods and tests</topic><topic>Indexing</topic><topic>Integration</topic><topic>Neurons - metabolism</topic><topic>Organs</topic><topic>Proteomics</topic><topic>Regulatory sequences</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Single-Cell Analysis</topic><topic>Specifications</topic><topic>Stem cell transplantation</topic><topic>Stem cells</topic><topic>Tissue analysis</topic><topic>Tissues</topic><topic>Transcription Factors - 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| source | American Association for the Advancement of Science; MEDLINE |
| subjects | Accessibility Adrenal glands Atlases as Topic Blood cells Cell differentiation Cell lines Chromatin Chromatin - metabolism Combinatorial analysis Data integration Developmental stages Embryogenesis Epigenetics Epithelial cells Erythropoiesis Fetus - cytology Fetus - metabolism Fetuses Gene expression Gene Expression Profiling Gene Expression Regulation, Developmental Genetics Hematopoietic stem cells Heterogeneity Human tissues Humans In vivo methods and tests Indexing Integration Neurons - metabolism Organs Proteomics Regulatory sequences Ribonucleic acid RNA Single-Cell Analysis Specifications Stem cell transplantation Stem cells Tissue analysis Tissues Transcription Factors - metabolism Websites |
| title | A human cell atlas of fetal gene expression |
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