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

By 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, Min Cho, Giana Cirolia, Stephanie D Conley, 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, Geraldine Genetiano, Xueying Gu, Gunsagar S. Gulati, Yan Hang, Shayan Hosseinzadeh, Albin Huang, Tal Iram, Taichi Isobe, Feather Ives, 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, Kaia L. May, Oliver L. May, Marina McKay, Ross J Metzger, Marco Mignardi, Dullei Min, Ahmad N. Nabhan, Katharine M Ng, Joseph Noh, Rasika Patkar, Weng Chuan Peng, Robert Puccinelli, Eric J. Rulifson, Shaheen S. Sikandar, Rahul Sinha, 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, Macy E Zardeneta, Fan Zhang, Lu Zhou, Paola Castro, Derek Croote, Joseph DeRisi, Angela Pisco, Bernhard M. Kiss, Christin S Kuo, Benoit Lehallier, Patricia K. Nguyen, Serena Y. Tan, Bruce M. Wang, Hanadie Yousef, Philip A. Beachy, Charles K. F. Chan, Kerwyn Casey Huang, Kenneth Weinberg, Sean Wu, Ben A. Barres, Michael F Clarke, Seung K Kim, Mark A Krasnow, Norma F. Neff, Roeland Nusse, Thomas A. Rando, Justin Sonnenburg, Irving L. Weissman, Sean M. Wu

Posted 20 Dec 2017
bioRxiv DOI: 10.1101/237446

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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