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Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris

Nicholas Schaum, Jim Karkanias, Norma F Neff, Andrew P. May, Stephen R. Quake, Tony Wyss-Coray, Spyros Darmanis, Joshua Batson, Olga Botvinnik, Michelle B. Chen, Steven Chen, Foad Green, Robert Jones, Ashley Maynard, Lolita Penland, Rene V. Sit, Geoffrey M. Stanley, James T. Webber, Fabio Zanini, Ankit S. Baghel, Isaac Bakerman, Ishita Bansal, Daniela Berdnik, Biter Bilen, Douglas Brownfield, Corey Cain, Michelle B. Chen, Steven Chen, Min Cho, Giana Cirolia, Stephanie D. Conley, Spyros Darmanis, Aaron Demers, Kubilay Demir, Antoine de Morree, Tessa Divita, Haley du Bois, Laughing Bear Torrez Dulgeroff, Hamid Ebadi, F. Hernan Espinoza, Matt Fish, Qiang Gan, Benson M. George, Astrid Gillich, Foad Green, Geraldine Genetiano, Xueying Gu, Gunsagar S. Gulati, Yan Hang, Shayan Hosseinzadeh, Albin Huang, Tal Iram, Taichi Isobe, Feather Ives, Robert Jones, Kevin S. Kao, Guruswamy Karnam, Aaron M. Kershner, Bernhard Kiss, William Kong, Maya E. Kumar, Jonathan Lam, Davis P. Lee, Song E. Lee, Guang Li, Qingyun Li, Ling Liu, Annie Lo, Wan-Jin Lu, Anoop Manjunath, Andrew P. May, Kaia L. May, Oliver L. May, Ashley Maynard, Marina McKay, Ross J. Metzger, Marco Mignardi, Dullei Min, Ahmad N. Nabhan, Norma F Neff, Katharine M. Ng, Joseph Noh, Rasika Patkar, Weng Chuan Peng, Lolita Penland, Robert Puccinelli, Eric J. Rulifson, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Rene V Sit, Krzysztof Szade, Weilun Tan, Cristina Tato, Krissie Tellez, Kyle J. Travaglini, Carolina Tropini, Lucas Waldburger, Linda J. van Weele, Michael N. Wosczyna, Jinyi Xiang, Soso Xue, Justin Youngyunpipatkul, Fabio Zanini, Macy E. Zardeneta, Fan Zhang, Lu Zhou, Ishita Bansal, Steven Chen, Min Cho, Giana Cirolia, Spyros Darmanis, Aaron Demers, Tessa Divita, Hamid Ebadi, Geraldine Genetiano, Foad Green, Shayan Hosseinzadeh, Feather Ives, Annie Lo, Andrew P. May, Ashley Maynard, Marina McKay, Norma F. Neff, Lolita Penland, Rene V. Sit, Weilun Tan, Lucas Waldburger, Justin Youngyunpipatkul, Joshua Batson, Olga Botvinnik, Paola Castro, Derek Croote, Spyros Darmanis, Joseph L. DeRisi, Jim Karkanias, Angela Pisco, Geoffrey M. Stanley, James T. Webber, Fabio Zanini, Ankit S. Baghel, Isaac Bakerman, Joshua Batson, Biter Bilen, Olga Botvinnik, Douglas Brownfield, Michelle B. Chen, Spyros Darmanis, Kubilay Demir, Antoine de Morree, Hamid Ebadi, F. Hernan Espinoza, Matt Fish, Qiang Gan, Benson M. George, Astrid Gillich, Xueying Gu, Gunsagar S. Gulati, Yan Hang, Albin Huang, Tal Iram, Taichi Isobe, Guruswamy Karnam, Aaron M. Kershner, Bernhard M. Kiss, William Kong, Christin S. Kuo, Jonathan Lam, Benoit Lehallier, Guang Li, Qingyun Li, Ling Liu, Wan-Jin Lu, Dullei Min, Ahmad N. Nabhan, Katharine M. Ng, Patricia K. Nguyen, Rasika Patkar, Weng Chuan Peng, Lolita Penland, Eric J. Rulifson, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Krzysztof Szade, Serena Y. Tan, Krissie Tellez, Kyle J. Travaglini, Carolina Tropini, Linda J. van Weele, Bruce M. Wang, Michael N. Wosczyna, Jinyi Xiang, Hanadie Yousef, Lu Zhou, Joshua Batson, Olga Botvinnik, Steven Chen, Spyros Darmanis, Foad Green, Andrew P. May, Ashley Maynard, Angela Pisco, Stephen R. Quake, Nicholas Schaum, Geoffrey M. Stanley, James T. Webber, Tony Wyss-Coray, Fabio Zanini, Philip A. Beachy, Charles K. F. Chan, Antoine de Morree, Benson M. George, Gunsagar S. Gulati, Yan Hang, Kerwyn Casey Huang, Tal Iram, Taichi Isobe, Aaron M. Kershner, Bernhard M. Kiss, William Kong, Guang Li, Qingyun Li, Ling Liu, Wan-Jin Lu, Ahmad N. Nabhan, Katharine M. Ng, Patricia K. Nguyen, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Krzysztof Szade, Kyle J. Travaglini, Carolina Tropini, Bruce M. Wang, Kenneth Weinberg, Michael N. Wosczyna, Sean Wu, Hanadie Yousef, Ben A. Barres, Philip A. Beachy, Charles K. F. Chan, Michael F. Clarke, Spyros Darmanis, Kerwyn Casey Huang, Jim Karkanias, Seung K. Kim, Mark A. Krasnow, Christin S. Kuo, Andrew P. May, Norma Neff, Roel Nusse, Patricia K. Nguyen, Thomas A. Rando, Justin Sonnenburg, Bruce M. Wang, Kenneth Weinberg, Irving L. Weissman, Sean M. Wu, Stephen R. Quake, Tony Wyss-Coray
doi: https://doi.org/10.1101/237446
Nicholas Schaum
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Jim Karkanias
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Norma F Neff
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Andrew P. May
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Stephen R. Quake
2Chan Zuckerburg Biohub, San Francisco, California, USA
3Department of Bioengineering, Stanford University, Stanford, California, USA
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  • For correspondence: quake@stanford.edu twc@stanford.edu s@czbiohub.org
Tony Wyss-Coray
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
5Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA
6Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
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  • For correspondence: quake@stanford.edu twc@stanford.edu s@czbiohub.org
Spyros Darmanis
2Chan Zuckerburg Biohub, San Francisco, California, USA
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  • For correspondence: quake@stanford.edu twc@stanford.edu s@czbiohub.org
Joshua Batson
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Olga Botvinnik
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Michelle B. Chen
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Steven Chen
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Foad Green
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Robert Jones
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Ashley Maynard
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Lolita Penland
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Rene V. Sit
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Geoffrey M. Stanley
3Department of Bioengineering, Stanford University, Stanford, California, USA
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James T. Webber
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Fabio Zanini
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Ankit S. Baghel
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Isaac Bakerman
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
7Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
8Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
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Ishita Bansal
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Daniela Berdnik
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Biter Bilen
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Douglas Brownfield
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Corey Cain
10Flow Cytometry Core, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
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Michelle B. Chen
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Steven Chen
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Min Cho
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Giana Cirolia
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Stephanie D. Conley
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Spyros Darmanis
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Aaron Demers
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Kubilay Demir
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
11Howard Hughes Medical Institute, USA
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Antoine de Morree
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Tessa Divita
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Haley du Bois
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Laughing Bear Torrez Dulgeroff
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Hamid Ebadi
2Chan Zuckerburg Biohub, San Francisco, California, USA
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F. Hernan Espinoza
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Matt Fish
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
11Howard Hughes Medical Institute, USA
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Qiang Gan
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Benson M. George
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Astrid Gillich
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Foad Green
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Geraldine Genetiano
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Xueying Gu
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Gunsagar S. Gulati
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Yan Hang
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Shayan Hosseinzadeh
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Albin Huang
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Tal Iram
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Taichi Isobe
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Feather Ives
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Robert Jones
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Kevin S. Kao
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Guruswamy Karnam
13Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
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Aaron M. Kershner
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Bernhard Kiss
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
14Department of Urology, Stanford University School of Medicine, Stanford, California, USA
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William Kong
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Maya E. Kumar
15Sean N. Parker Center for Asthma and Allergy Research, Stanford University School of Medicine, Stanford, California, USA
16Department of Medicine, Division of Pulmonary and Critical Care, Stanford University School of Medicine, Stanford, California, USA
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Jonathan Lam
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Davis P. Lee
6Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
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Song E. Lee
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Guang Li
17Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
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Qingyun Li
18Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
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Ling Liu
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Annie Lo
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Wan-Jin Lu
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Anoop Manjunath
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Andrew P. May
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Kaia L. May
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Oliver L. May
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Ashley Maynard
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Marina McKay
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Ross J. Metzger
19Vera Moulton Wall Center for Pulmonary and Vascular Disease, Stanford University School of Medicine, Stanford, California, USA
20Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
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Marco Mignardi
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Dullei Min
21Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
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Ahmad N. Nabhan
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Norma F Neff
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Katharine M. Ng
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Joseph Noh
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Rasika Patkar
13Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
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Weng Chuan Peng
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Lolita Penland
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Robert Puccinelli
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Eric J. Rulifson
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Nicholas Schaum
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Shaheen S. Sikandar
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Rahul Sinha
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
22Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
23Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, California, USA
24Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
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Rene V Sit
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Krzysztof Szade
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
25Department of Medical Biotechnology, Faculty of Biophysics, Biochemistry and Biotechnology, Jagiellonian University, Poland
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Weilun Tan
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Cristina Tato
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Krissie Tellez
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Kyle J. Travaglini
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Carolina Tropini
26Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
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Lucas Waldburger
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Linda J. van Weele
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Michael N. Wosczyna
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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Jinyi Xiang
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Soso Xue
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Justin Youngyunpipatkul
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Fabio Zanini
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Macy E. Zardeneta
6Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
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Fan Zhang
19Vera Moulton Wall Center for Pulmonary and Vascular Disease, Stanford University School of Medicine, Stanford, California, USA
20Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
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Lu Zhou
18Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
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Ishita Bansal
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Steven Chen
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Min Cho
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3Department of Bioengineering, Stanford University, Stanford, California, USA
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7Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
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11Howard Hughes Medical Institute, USA
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11Howard Hughes Medical Institute, USA
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9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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11Howard Hughes Medical Institute, USA
21Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
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17Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
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18Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
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9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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21Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
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7Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
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17Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
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13Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
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23Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, California, USA
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25Department of Medical Biotechnology, Faculty of Biophysics, Biochemistry and Biotechnology, Jagiellonian University, Poland
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22Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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26Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
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13Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
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18Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
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2Chan Zuckerburg Biohub, San Francisco, California, USA
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2Chan Zuckerburg Biohub, San Francisco, California, USA
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2Chan Zuckerburg Biohub, San Francisco, California, USA
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Tony Wyss-Coray
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
5Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA
6Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
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3Department of Bioengineering, Stanford University, Stanford, California, USA
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Philip A. Beachy
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
11Howard Hughes Medical Institute, USA
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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28Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, California USA
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12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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2Chan Zuckerburg Biohub, San Francisco, California, USA
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26Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
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4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
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14Department of Urology, Stanford University School of Medicine, Stanford, California, USA
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17Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
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18Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
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4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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3Department of Bioengineering, Stanford University, Stanford, California, USA
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1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
7Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
8Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
17Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
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Rahul Sinha
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
22Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
23Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, California, USA
24Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
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Krzysztof Szade
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
25Department of Medical Biotechnology, Faculty of Biophysics, Biochemistry and Biotechnology, Jagiellonian University, Poland
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9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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26Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
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13Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
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21Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
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4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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17Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
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4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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18Department of Neurobiology, Stanford University School of Medicine, Stanford, CA USA
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Philip A. Beachy
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
11Howard Hughes Medical Institute, USA
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Charles K. F. Chan
28Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, California USA
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Michael F. Clarke
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Spyros Darmanis
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Kerwyn Casey Huang
2Chan Zuckerburg Biohub, San Francisco, California, USA
3Department of Bioengineering, Stanford University, Stanford, California, USA
26Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
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Jim Karkanias
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Seung K. Kim
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
29Department of Medicine and Stanford Diabetes Research Center, Stanford University, Stanford, California USA
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Mark A. Krasnow
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
11Howard Hughes Medical Institute, USA
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Christin S. Kuo
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
11Howard Hughes Medical Institute, USA
21Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
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Andrew P. May
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Norma Neff
2Chan Zuckerburg Biohub, San Francisco, California, USA
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Roel Nusse
9Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
11Howard Hughes Medical Institute, USA
12Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Patricia K. Nguyen
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
7Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
8Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, USA
17Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
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Thomas A. Rando
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
5Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA
6Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
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Justin Sonnenburg
26Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
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Bruce M. Wang
13Department of Medicine and Liver Center, University of California San Francisco, San Francisco, California, USA
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Kenneth Weinberg
21Department of Pediatrics, Stanford University school of Medicine, Stanford, California, USA
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Irving L. Weissman
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
22Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
23Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, California, USA
24Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
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Sean M. Wu
1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
7Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
17Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
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Stephen R. Quake
2Chan Zuckerburg Biohub, San Francisco, California, USA
3Department of Bioengineering, Stanford University, Stanford, California, USA
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Tony Wyss-Coray
4Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
5Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA
6Center for Tissue Regeneration, Repair, and Restoration, V.A. Palo Alto Healthcare System, Palo Alto, California, USA
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  • Abstract
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The Tabula Muris Consortium

We have created a compendium of single cell transcriptome data from the model organism Mus musculus comprising more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, revealing gene expression in poorly characterized cell populations and allowing for direct and controlled comparison of gene expression in cell types shared between tissues, such as T-lymphocytes and endothelial cells from distinct anatomical locations. Two distinct technical approaches were used for most tissues: one approach, microfluidic droplet-based 3’-end counting, enabled the survey of thousands of cells at relatively low coverage, while the other, FACS-based full length transcript analysis, enabled characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

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  • Author Information Reprints and permissions information is available at www.nature.com/reprints. The authors declare no completing financial interests: the details are available in the online version of the paper. Readers are welcome to comment on the online version of the paper.

  • Reviewer Information Nature thanks the anonymous reviewers for their contributions to the peer review of this work.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris
Nicholas Schaum, Jim Karkanias, Norma F Neff, Andrew P. May, Stephen R. Quake, Tony Wyss-Coray, Spyros Darmanis, Joshua Batson, Olga Botvinnik, Michelle B. Chen, Steven Chen, Foad Green, Robert Jones, Ashley Maynard, Lolita Penland, Rene V. Sit, Geoffrey M. Stanley, James T. Webber, Fabio Zanini, Ankit S. Baghel, Isaac Bakerman, Ishita Bansal, Daniela Berdnik, Biter Bilen, Douglas Brownfield, Corey Cain, Michelle B. Chen, Steven Chen, Min Cho, Giana Cirolia, Stephanie D. Conley, Spyros Darmanis, Aaron Demers, Kubilay Demir, Antoine de Morree, Tessa Divita, Haley du Bois, Laughing Bear Torrez Dulgeroff, Hamid Ebadi, F. Hernan Espinoza, Matt Fish, Qiang Gan, Benson M. George, Astrid Gillich, Foad Green, Geraldine Genetiano, Xueying Gu, Gunsagar S. Gulati, Yan Hang, Shayan Hosseinzadeh, Albin Huang, Tal Iram, Taichi Isobe, Feather Ives, Robert Jones, Kevin S. Kao, Guruswamy Karnam, Aaron M. Kershner, Bernhard Kiss, William Kong, Maya E. Kumar, Jonathan Lam, Davis P. Lee, Song E. Lee, Guang Li, Qingyun Li, Ling Liu, Annie Lo, Wan-Jin Lu, Anoop Manjunath, Andrew P. May, Kaia L. May, Oliver L. May, Ashley Maynard, Marina McKay, Ross J. Metzger, Marco Mignardi, Dullei Min, Ahmad N. Nabhan, Norma F Neff, Katharine M. Ng, Joseph Noh, Rasika Patkar, Weng Chuan Peng, Lolita Penland, Robert Puccinelli, Eric J. Rulifson, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Rene V Sit, Krzysztof Szade, Weilun Tan, Cristina Tato, Krissie Tellez, Kyle J. Travaglini, Carolina Tropini, Lucas Waldburger, Linda J. van Weele, Michael N. Wosczyna, Jinyi Xiang, Soso Xue, Justin Youngyunpipatkul, Fabio Zanini, Macy E. Zardeneta, Fan Zhang, Lu Zhou, Ishita Bansal, Steven Chen, Min Cho, Giana Cirolia, Spyros Darmanis, Aaron Demers, Tessa Divita, Hamid Ebadi, Geraldine Genetiano, Foad Green, Shayan Hosseinzadeh, Feather Ives, Annie Lo, Andrew P. May, Ashley Maynard, Marina McKay, Norma F. Neff, Lolita Penland, Rene V. Sit, Weilun Tan, Lucas Waldburger, Justin Youngyunpipatkul, Joshua Batson, Olga Botvinnik, Paola Castro, Derek Croote, Spyros Darmanis, Joseph L. DeRisi, Jim Karkanias, Angela Pisco, Geoffrey M. Stanley, James T. Webber, Fabio Zanini, Ankit S. Baghel, Isaac Bakerman, Joshua Batson, Biter Bilen, Olga Botvinnik, Douglas Brownfield, Michelle B. Chen, Spyros Darmanis, Kubilay Demir, Antoine de Morree, Hamid Ebadi, F. Hernan Espinoza, Matt Fish, Qiang Gan, Benson M. George, Astrid Gillich, Xueying Gu, Gunsagar S. Gulati, Yan Hang, Albin Huang, Tal Iram, Taichi Isobe, Guruswamy Karnam, Aaron M. Kershner, Bernhard M. Kiss, William Kong, Christin S. Kuo, Jonathan Lam, Benoit Lehallier, Guang Li, Qingyun Li, Ling Liu, Wan-Jin Lu, Dullei Min, Ahmad N. Nabhan, Katharine M. Ng, Patricia K. Nguyen, Rasika Patkar, Weng Chuan Peng, Lolita Penland, Eric J. Rulifson, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Krzysztof Szade, Serena Y. Tan, Krissie Tellez, Kyle J. Travaglini, Carolina Tropini, Linda J. van Weele, Bruce M. Wang, Michael N. Wosczyna, Jinyi Xiang, Hanadie Yousef, Lu Zhou, Joshua Batson, Olga Botvinnik, Steven Chen, Spyros Darmanis, Foad Green, Andrew P. May, Ashley Maynard, Angela Pisco, Stephen R. Quake, Nicholas Schaum, Geoffrey M. Stanley, James T. Webber, Tony Wyss-Coray, Fabio Zanini, Philip A. Beachy, Charles K. F. Chan, Antoine de Morree, Benson M. George, Gunsagar S. Gulati, Yan Hang, Kerwyn Casey Huang, Tal Iram, Taichi Isobe, Aaron M. Kershner, Bernhard M. Kiss, William Kong, Guang Li, Qingyun Li, Ling Liu, Wan-Jin Lu, Ahmad N. Nabhan, Katharine M. Ng, Patricia K. Nguyen, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Krzysztof Szade, Kyle J. Travaglini, Carolina Tropini, Bruce M. Wang, Kenneth Weinberg, Michael N. Wosczyna, Sean Wu, Hanadie Yousef, Ben A. Barres, Philip A. Beachy, Charles K. F. Chan, Michael F. Clarke, Spyros Darmanis, Kerwyn Casey Huang, Jim Karkanias, Seung K. Kim, Mark A. Krasnow, Christin S. Kuo, Andrew P. May, Norma Neff, Roel Nusse, Patricia K. Nguyen, Thomas A. Rando, Justin Sonnenburg, Bruce M. Wang, Kenneth Weinberg, Irving L. Weissman, Sean M. Wu, Stephen R. Quake, Tony Wyss-Coray
bioRxiv 237446; doi: https://doi.org/10.1101/237446
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Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris
Nicholas Schaum, Jim Karkanias, Norma F Neff, Andrew P. May, Stephen R. Quake, Tony Wyss-Coray, Spyros Darmanis, Joshua Batson, Olga Botvinnik, Michelle B. Chen, Steven Chen, Foad Green, Robert Jones, Ashley Maynard, Lolita Penland, Rene V. Sit, Geoffrey M. Stanley, James T. Webber, Fabio Zanini, Ankit S. Baghel, Isaac Bakerman, Ishita Bansal, Daniela Berdnik, Biter Bilen, Douglas Brownfield, Corey Cain, Michelle B. Chen, Steven Chen, Min Cho, Giana Cirolia, Stephanie D. Conley, Spyros Darmanis, Aaron Demers, Kubilay Demir, Antoine de Morree, Tessa Divita, Haley du Bois, Laughing Bear Torrez Dulgeroff, Hamid Ebadi, F. Hernan Espinoza, Matt Fish, Qiang Gan, Benson M. George, Astrid Gillich, Foad Green, Geraldine Genetiano, Xueying Gu, Gunsagar S. Gulati, Yan Hang, Shayan Hosseinzadeh, Albin Huang, Tal Iram, Taichi Isobe, Feather Ives, Robert Jones, Kevin S. Kao, Guruswamy Karnam, Aaron M. Kershner, Bernhard Kiss, William Kong, Maya E. Kumar, Jonathan Lam, Davis P. Lee, Song E. Lee, Guang Li, Qingyun Li, Ling Liu, Annie Lo, Wan-Jin Lu, Anoop Manjunath, Andrew P. May, Kaia L. May, Oliver L. May, Ashley Maynard, Marina McKay, Ross J. Metzger, Marco Mignardi, Dullei Min, Ahmad N. Nabhan, Norma F Neff, Katharine M. Ng, Joseph Noh, Rasika Patkar, Weng Chuan Peng, Lolita Penland, Robert Puccinelli, Eric J. Rulifson, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Rene V Sit, Krzysztof Szade, Weilun Tan, Cristina Tato, Krissie Tellez, Kyle J. Travaglini, Carolina Tropini, Lucas Waldburger, Linda J. van Weele, Michael N. Wosczyna, Jinyi Xiang, Soso Xue, Justin Youngyunpipatkul, Fabio Zanini, Macy E. Zardeneta, Fan Zhang, Lu Zhou, Ishita Bansal, Steven Chen, Min Cho, Giana Cirolia, Spyros Darmanis, Aaron Demers, Tessa Divita, Hamid Ebadi, Geraldine Genetiano, Foad Green, Shayan Hosseinzadeh, Feather Ives, Annie Lo, Andrew P. May, Ashley Maynard, Marina McKay, Norma F. Neff, Lolita Penland, Rene V. Sit, Weilun Tan, Lucas Waldburger, Justin Youngyunpipatkul, Joshua Batson, Olga Botvinnik, Paola Castro, Derek Croote, Spyros Darmanis, Joseph L. DeRisi, Jim Karkanias, Angela Pisco, Geoffrey M. Stanley, James T. Webber, Fabio Zanini, Ankit S. Baghel, Isaac Bakerman, Joshua Batson, Biter Bilen, Olga Botvinnik, Douglas Brownfield, Michelle B. Chen, Spyros Darmanis, Kubilay Demir, Antoine de Morree, Hamid Ebadi, F. Hernan Espinoza, Matt Fish, Qiang Gan, Benson M. George, Astrid Gillich, Xueying Gu, Gunsagar S. Gulati, Yan Hang, Albin Huang, Tal Iram, Taichi Isobe, Guruswamy Karnam, Aaron M. Kershner, Bernhard M. Kiss, William Kong, Christin S. Kuo, Jonathan Lam, Benoit Lehallier, Guang Li, Qingyun Li, Ling Liu, Wan-Jin Lu, Dullei Min, Ahmad N. Nabhan, Katharine M. Ng, Patricia K. Nguyen, Rasika Patkar, Weng Chuan Peng, Lolita Penland, Eric J. Rulifson, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Krzysztof Szade, Serena Y. Tan, Krissie Tellez, Kyle J. Travaglini, Carolina Tropini, Linda J. van Weele, Bruce M. Wang, Michael N. Wosczyna, Jinyi Xiang, Hanadie Yousef, Lu Zhou, Joshua Batson, Olga Botvinnik, Steven Chen, Spyros Darmanis, Foad Green, Andrew P. May, Ashley Maynard, Angela Pisco, Stephen R. Quake, Nicholas Schaum, Geoffrey M. Stanley, James T. Webber, Tony Wyss-Coray, Fabio Zanini, Philip A. Beachy, Charles K. F. Chan, Antoine de Morree, Benson M. George, Gunsagar S. Gulati, Yan Hang, Kerwyn Casey Huang, Tal Iram, Taichi Isobe, Aaron M. Kershner, Bernhard M. Kiss, William Kong, Guang Li, Qingyun Li, Ling Liu, Wan-Jin Lu, Ahmad N. Nabhan, Katharine M. Ng, Patricia K. Nguyen, Nicholas Schaum, Shaheen S. Sikandar, Rahul Sinha, Krzysztof Szade, Kyle J. Travaglini, Carolina Tropini, Bruce M. Wang, Kenneth Weinberg, Michael N. Wosczyna, Sean Wu, Hanadie Yousef, Ben A. Barres, Philip A. Beachy, Charles K. F. Chan, Michael F. Clarke, Spyros Darmanis, Kerwyn Casey Huang, Jim Karkanias, Seung K. Kim, Mark A. Krasnow, Christin S. Kuo, Andrew P. May, Norma Neff, Roel Nusse, Patricia K. Nguyen, Thomas A. Rando, Justin Sonnenburg, Bruce M. Wang, Kenneth Weinberg, Irving L. Weissman, Sean M. Wu, Stephen R. Quake, Tony Wyss-Coray
bioRxiv 237446; doi: https://doi.org/10.1101/237446

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