1. Publications

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Tabula Sapiens Consortium*; Robert C Jones, Jim Karkanias, Mark A Krasnow, Angela Oliveira Pisco, Stephen R Quake, Julia Salzman, Nir Yosef, Bryan Bulthaup, Phillip Brown, William Harper, Marisa Hemenez, Ravikumar Ponnusamy, Ahmad Salehi, Bhavani A Sanagavarapu, Eileen Spallino, Ksenia A Aaron, Waldo Concepcion, James M Gardner, Burnett Kelly, Nikole Neidlinger, Zifa Wang, Sheela Crasta, Saroja Kolluru, Maurizio Morri, Angela Oliveira Pisco, Serena Y Tan, Kyle J Travaglini, Chenling Xu, Marcela Alcántara-Hernández, Nicole Almanzar, Jane Antony, Benjamin Beyersdorf, Deviana Burhan, Kruti Calcuttawala, Matthew M Carter, Charles K F Chan, Charles A Chang, Stephen Chang, Alex Colville, Sheela Crasta, Rebecca N Culver, Ivana Cvijović, Gaetano D'Amato, Camille Ezran, Francisco X Galdos, Astrid Gillich, William R Goodyer, Yan Hang, Alyssa Hayashi, Sahar Houshdaran, Xianxi Huang, Juan C Irwin, SoRi Jang, Julia Vallve Juanico, Aaron M Kershner, Soochi Kim, Bernhard Kiss, Saroja Kolluru, William Kong, Maya E Kumar, Angera H Kuo, Rebecca Leylek, Baoxiang Li, Gabriel B Loeb, Wan-Jin Lu, Sruthi Mantri, Maxim Markovic, Patrick L McAlpine, Antoine de Morree, Maurizio Morri, Karim Mrouj, Shravani Mukherjee, Tyler Muser, Patrick Neuhöfer, Thi D Nguyen, Kimberly Perez, Ragini Phansalkar, Angela Oliveira Pisco, Nazan Puluca, Zhen Qi, Poorvi Rao, Hayley Raquer-McKay, Nicholas Schaum, Bronwyn Scott, Bobak Seddighzadeh, Joe Segal, Sushmita Sen, Shaheen Sikandar, Sean P Spencer, Lea C Steffes, Varun R Subramaniam, Aditi Swarup, Michael Swift, Kyle J Travaglini, Will Van Treuren, Emily Trimm, Stefan Veizades, Sivakamasundari Vijayakumar, Kim Chi Vo, Sevahn K Vorperian, Wanxin Wang, Hannah N W Weinstein, Juliane Winkler, Timothy T H Wu, Jamie Xie, Andrea R Yung, Yue Zhang, Angela M Detweiler, Honey Mekonen, Norma F Neff, Rene V Sit, Michelle Tan, Jia Yan, Gregory R Bean, Vivek Charu, Erna Forgó, Brock A Martin, Michael G Ozawa, Oscar Silva, Serena Y Tan, Angus Toland, Venkata N P Vemuri, Shaked Afik, Kyle Awayan, Olga Borisovna Botvinnik, Ashley Byrne, Michelle Chen, Roozbeh Dehghannasiri, Angela M Detweiler, Adam Gayoso, Alejandro A Granados, Qiqing Li, Gita Mahmoudabadi, Aaron McGeever, Antoine de Morree, Julia Eve Olivieri, Madeline Park, Angela Oliveira Pisco, Neha Ravikumar, Julia Salzman, Geoff Stanley, Michael Swift, Michelle Tan, Weilun Tan, Alexander J Tarashansky, Rohan Vanheusden, Sevahn K Vorperian, Peter Wang, Sheng Wang, Galen Xing, Chenling Xu, Nir Yosef, Marcela Alcántara-Hernández, Jane Antony, Charles K F Chan, Charles A Chang, Alex Colville, Sheela Crasta, Rebecca Culver, Les Dethlefsen, Camille Ezran, Astrid Gillich, Yan Hang, Po-Yi Ho, Juan C Irwin, SoRi Jang, Aaron M Kershner, William Kong, Maya E Kumar, Angera H Kuo, Rebecca Leylek, Shixuan Liu, Gabriel B Loeb, Wan-Jin Lu, Jonathan S Maltzman, Ross J Metzger, Antoine de Morree, Patrick Neuhöfer, Kimberly Perez, Ragini Phansalkar, Zhen Qi, Poorvi Rao, Hayley Raquer-McKay, Koki Sasagawa, Bronwyn Scott, Rahul Sinha, Hanbing Song, Sean P Spencer, Aditi Swarup, Michael Swift, Kyle J Travaglini, Emily Trimm, Stefan Veizades, Sivakamasundari Vijayakumar, Bruce Wang, Wanxin Wang, Juliane Winkler, Jamie Xie, Andrea R Yung, Steven E Artandi, Philip A Beachy, Michael F Clarke, Linda C Giudice, Franklin W Huang, Kerwyn Casey Huang, Juliana Idoyaga, Seung K Kim, Mark Krasnow, Christin S Kuo, Patricia Nguyen, Stephen R Quake, Thomas A Rando, Kristy Red-Horse, Jeremy Reiter, David A Relman, Justin L Sonnenburg, Bruce Wang, Albert Wu, Sean M Wu, Tony Wyss-Coray.
Science. 2022-05-13;376(6594):eabl4896.
Abstract
Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Related data

Available data
website
Data summary
The entire dataset can be explored interactively at http://tabula-sapiens-portal.ds.czbiohub.org/.
Available data
website
Data summary
The code used for the analysis is available from Zenodo (https://doi.org/10.5281/zenodo.6069683).
Available data
website
Data summary
Gene counts and metadata are available from figshare (https://doi.org/10.6084/m9.figshare.14267219) and have been deposited in the Gene Expression Omnibus (GSE149590).
Available data
website
Data summary
The raw data files are available from a public AWS S3 bucket (https://registry.opendata.aws/tabula-sapiens/) and instructions on how to access the data have been provided in the project GitHub.
Available data
website
Data summary
The histology images are available from figshare (https://doi.org/10.6084/m9.figshare.14962947).
Available data
website
Data summary
SpliZ scores are available from figshare (https://doi.org/10.6084/m9.figshare.14977281).