Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

被引：1826

作者：

Schaum, Nicholas ^{[1
]}

Karkanias, Jim ^{[2
]}

Neff, Norma F. ^{[2
]}

May, Andrew P. ^{[2
]}

Quake, Stephen R. ^{[2
,3
]}

Wyss-Coray, Tony ^{[4
,5
,6
]}

Darmanis, Spyros ^{[2
]}

Batson, Joshua ^{[2
]}

Botvinnik, Olga ^{[2
]}

Chen, Michelle B. ^{[3
]}

Chen, Steven ^{[2
]}

Green, Foad ^{[2
]}

Jones, Robert C. ^{[3
]}

Maynard, Ashley ^{[2
]}

Penland, Lolita ^{[2
]}

Pisco, Angela Oliveira ^{[2
]}

Sit, Rene V. ^{[2
]}

Stanley, Geoffrey M. ^{[3
]}

Webber, James T. ^{[2
]}

Zanini, Fabio ^{[3
]}

Baghel, Ankit S. ^{[1
]}

Bakerman, Isaac ^{[1
,7
,8
]}

Bansal, Ishita ^{[2
]}

Berdnik, Daniela ^{[4
]}

Bilen, Biter ^{[4
]}

Brownfield, Douglas ^{[9
]}

Cain, Corey ^{[10
]}

Cho, Min ^{[2
]}

Cirolia, Giana ^{[2
]}

Conley, Stephanie D. ^{[1
]}

Demers, Aaron ^{[2
,3
]}

Demir, Kubilay ^{[1
,11
]}

de Morree, Antoine ^{[4
]}

Divita, Tessa ^{[2
]}

du Bois, Haley ^{[4
]}

Dulgeroff, Laughing Bear Torrez ^{[1
]}

Ebadi, Hamid ^{[2
]}

Espinoza, F. Hernan ^{[9
]}

Fish, Matt ^{[1
,11
,12
]}

Gan, Qiang ^{[4
]}

George, Benson M. ^{[1
]}

Gillich, Astrid ^{[9
]}

Genetiano, Geraldine ^{[2
]}

Gu, Xueying ^{[12
]}

Gulati, Gunsagar S. ^{[1
]}

Hang, Yan ^{[12
]}

Hosseinzadeh, Shayan ^{[2
]}

Huang, Albin ^{[4
]}

Iram, Tal ^{[4
]}

Isobe, Taichi ^{[1
]}

机构：

[1] Stanford Univ, Sch Med, Inst Stem Cell Biol & Regenerat Med, Stanford, CA 94305 USA

[2] Chan Zuckerberg Biohub, San Francisco, CA 94158 USA

[3] Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA

[4] Stanford Univ, Sch Med, Dept Neurol & Neurol Sci, Stanford, CA 94305 USA

[5] Stanford Univ, Sch Med, Paul F Glenn Ctr Biol Aging, Stanford, CA 94305 USA

[6] VA Palo Alto Healthcare Syst, Ctr Tissue Regenerat Repair & Restorat, Palo Alto, CA 94304 USA

[7] Stanford Univ, Sch Med, Stanford Cardiovasc Inst, Stanford, CA 94305 USA

[8] Stanford Univ, Sch Med, Div Cardiol, Dept Med, Stanford, CA 94305 USA

[9] Stanford Univ, Sch Med, Dept Biochem, Stanford, CA 94305 USA

[10] VA Palo Alto Healthcare Syst, Flow Cytometry Core, Palo Alto, CA USA

[11] Stanford Univ, Howard Hughes Med Inst, Stanford, CA 94305 USA

[12] Stanford Univ, Sch Med, Dept Dev Biol, Stanford, CA 94305 USA

[13] Univ Calif San Francisco, Dept Med, San Francisco, CA 94143 USA

[14] Univ Calif San Francisco, Liver Ctr, San Francisco, CA 94143 USA

[15] Stanford Univ, Sch Med, Dept Urol, Stanford, CA 94305 USA

[16] Stanford Univ, Sch Med, Sean N Parker Ctr Asthma & Allergy Res, Stanford, CA 94305 USA

[17] Stanford Univ, Sch Med, Div Pulm & Crit Care, Dept Med, Stanford, CA 94305 USA

[18] Stanford Univ, Div Cardiovasc Med, Dept Med, Stanford, CA 94305 USA

[19] Stanford Univ, Sch Med, Dept Neurobiol, Stanford, CA 94305 USA

[20] Stanford Univ, Sch Med, Vera Moulton Wall Ctr Pulm & Vasc Dis, Stanford, CA 94305 USA

[21] Stanford Univ, Sch Med, Div Cardiol, Dept Pediat, Stanford, CA 94305 USA

[22] Stanford Univ, Sch Med, Pulm Med, Dept Pediat, Stanford, CA 94305 USA

[23] Stanford Univ, Sch Med, Dept Pathol, Stanford, CA 94305 USA

[24] Stanford Univ, Sch Med, Ludwig Ctr Canc Stem Cell Res & Med, Stanford, CA 94305 USA

[25] Stanford Univ, Sch Med, Stanford Canc Inst, Stanford, CA 94305 USA

[26] Jagiellonian Univ, Fac Biochem Biophys & Biotechnol, Dept Med Biotechnol, Krakow, Poland

[27] Stanford Univ, Sch Med, Dept Microbiol & Immunol, Stanford, CA 94305 USA

[28] Univ Calif San Francisco, Dept Biochem, San Francisco, CA 94143 USA

[29] Stanford Univ, Div Plast & Reconstruct Surg, Dept Surg, Stanford, CA 94305 USA

[30] Stanford Univ, Dept Med, Stanford, CA 94305 USA

[31] Stanford Univ, Stanford Diabet Res Ctr, Stanford, CA 94305 USA

来源：

NATURE | 2018年 / 562卷 / 7727期

基金：

美国国家卫生研究院;

关键词：

GENE-EXPRESSION; RNA-SEQ;

D O I：

10.1038/s41586-018-0590-4

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3'-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

引用

页码：367 / +

页数：20

共 30 条

[1]

Alberts B., 2016, Essential Cell Biology

[2]

Whole-organism clone tracing using single-cell sequencing [J].

Alemany, Anna ;

Florescu, Maria ;

Baron, Chloe S. ;

Peterson-Maduro, Josi ;

van Oudenaarden, Alexander .

NATURE, 2018, 556 (7699) :108-+

[3]

Cell type discovery and representation in the era of high-content single cell phenotyping [J].

Bakken, Trygve ;

Cowell, Lindsay ;

Aevermann, Brian D. ;

Novotny, Mark ;

Hodge, Rebecca ;

Miller, Jeremy A. ;

Lee, Alexandra ;

Chang, Ivan ;

McCorrison, Jamison ;

Pulendran, Bali ;

Qian, Yu ;

Schork, Nicholas J. ;

Lasken, Roger S. ;

Lein, Ed S. ;

Scheuermann, Richard H. .

BMC BIOINFORMATICS, 2017, 18

[4]

Comprehensive single-cell transcriptional profiling of a multicellular organism [J].

Cao, Junyue ;

Packer, Jonathan S. ;

Ramani, Vijay ;

Cusanovich, Darren A. ;

Huynh, Chau ;

Daza, Riza ;

Qiu, Xiaojie ;

Lee, Choli ;

Furlan, Scott N. ;

Steemers, Frank J. ;

Adey, Andrew ;

Waterston, Robert H. ;

Trapnell, Cole ;

Shendure, Jay .

SCIENCE, 2017, 357 (6352) :661-667

[5]

Single-cell dissection of transcriptional heterogeneity in human colon tumors [J].

Dalerba, Piero ;

Kalisky, Tomer ;

Sahoo, Debashis ;

Rajendran, Pradeep S. ;

Rothenberg, Michael E. ;

Leyrat, Anne A. ;

Sim, Sopheak ;

Okamoto, Jennifer ;

Johnston, Darius M. ;

Qian, Dalong ;

Zabala, Maider ;

Bueno, Janet ;

Neff, Norma F. ;

Wang, Jianbin ;

Shelton, Andrew A. ;

Visser, Brendan ;

Hisamori, Shigeo ;

Shimono, Yohei ;

van de Wetering, Marc ;

Clevers, Hans ;

Clarke, Michael F. ;

Quake, Stephen R. .

NATURE BIOTECHNOLOGY, 2011, 29 (12) :1120-U11

[6]

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma [J].

Darmanis, Spyros ;

Sloan, Steven A. ;

Croote, Derek ;

Mignardi, Marco ;

Chernikova, Sophia ;

Samghababi, Peyman ;

Zhang, Ye ;

Neff, Norma ;

Kowarsky, Mark ;

Caneda, Christine ;

Li, Gordon ;

Chang, Steven D. ;

Connolly, Ian David ;

Li, Yingmei ;

Barres, Ben A. ;

Gephart, Melanie Hayden ;

Quake, Stephen R. .

CELL REPORTS, 2017, 21 (05) :1399-1410

[7]

A survey of human brain transcriptome diversity at the single cell level [J].

Darmanis, Spyros ;

Sloan, Steven A. ;

Zhang, Ye ;

Enge, Martin ;

Caneda, Christine ;

Shuer, Lawrence M. ;

Gephart, Melanie G. Hayden ;

Barres, Ben A. ;

Quake, Stephen R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (23) :7285-7290

[8]

Gene selection and classification of microarray data using random forest -: art. no. 3 [J].

Díaz-Uriarte, R ;

de Andrés, SA .

BMC BIOINFORMATICS, 2006, 7 (1)

[9]

Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns [J].

Enge, Martin ;

Arda, Efsun ;

Mignardi, Marco ;

Beausang, John ;

Bottino, Rita ;

Kim, Seung K. ;

Quake, Stephen R. .

CELL, 2017, 171 (02) :321-+

[10]

Freytag Saskia, 2018, F1000Res, V7, P1297, DOI 10.12688/f1000research.15809.1

← 1 2 3 →