The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
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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.
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Universal cell atlases may serve as a powerful resource for modeling cellular behavior over longer timescales, such as tissue formation.
“The recent construction of universal cell atlases101,106 may serve as a powerful resource for modeling cellular behavior over longer timescales, such as tissue formation.”
From How to build the virtual cell with artificial intelligence: Priorities and opportunities (2024) · cites this paper as [106]
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- Authors
- The Tabula Sapiens Consortium*, Jones, R. C., Karkanias, J., Krasnow, M. A., Pisco, A. O., Quake, S. R., Salzman, J., Yosef, N., Bulthaup, B., Brown, P., Harper, W., Hemenez, M., Ponnusamy, R., Salehi, A., Sanagavarapu, B. A., Spallino, E., Aaron, K. A., Concepcion, W., Gardner, J. M., Kelly, B., Neidlinger, N., Wang, Z., Crasta, S., Kolluru, S., Morri, M., Tan, S. Y., Travaglini, K. J., Xu, C., Alcántara-Hernández, M., Almanzar, N., Antony, J., Beyersdorf, B., Burhan, D., Calcuttawala, K., Carter, M. M., Chan, C. K. F., Chang, C. A., Chang, S., Colville, A., Culver, R. N., Cvijović, I., D’Amato, G., Ezran, C., Galdos, F. X., Gillich, A., Goodyer, W. R., Hang, Y., Hayashi, A., Houshdaran, S., Huang, X., Irwin, J. C., Jang, S., Juanico, J. V., Kershner, A. M., Kim, S., Kiss, B., Kong, W., Kumar, M. E., Kuo, A. H., Leylek, R., Li, B., Loeb, G. B., Lu, W.-J., Mantri, S., Markovic, M., McAlpine, P. L., de Morree, A., Mrouj, K., Mukherjee, S., Muser, T., Neuhöfer, P., Nguyen, T. D., Perez, K., Phansalkar, R., Puluca, N., Qi, Z., Rao, P., Raquer-McKay, H., Schaum, N., Scott, B., Seddighzadeh, B., Segal, J., Sen, S., Sikandar, S., Spencer, S. P., Steffes, L. C., Subramaniam, V. R., Swarup, A., Swift, M., Van Treuren, W., Trimm, E., Veizades, S., Vijayakumar, S., Vo, K. C., Vorperian, S. K., Wang, W., Weinstein, H. N. W., Winkler, J., Wu, T. T. H., Xie, J., Yung, A. R., Zhang, Y., Detweiler, A. M., Mekonen, H., Neff, N. F., Sit, R. V., Tan, M., Yan, J., Bean, G. R., Charu, V., Forgó, E., Martin, B. A., Ozawa, M. G., Silva, O., Toland, A., Vemuri, V. N. P., Afik, S., Awayan, K., Botvinnik, O. B., Byrne, A., Chen, M., Dehghannasiri, R., Gayoso, A., Granados, A. A., Li, Q., Mahmoudabadi, G., McGeever, A., Olivieri, J. E., Park, M., Ravikumar, N., Stanley, G., Tan, W., Tarashansky, A. J., Vanheusden, R., Wang, P., Wang, S., Xing, G., Dethlefsen, L., Ho, P.-Y., Liu, S., Maltzman, J. S., Metzger, R. J., Sasagawa, K., Sinha, R., Song, H., Wang, B., Artandi, S. E., Beachy, P. A., Clarke, M. F., Giudice, L. C., Huang, F. W., Huang, K. C., Idoyaga, J., Kim, S. K., Kuo, C. S., Nguyen, P., Rando, T. A., Red-Horse, K., Reiter, J., Relman, D. A., Sonnenburg, J. L., Wu, A., Wu, S. M., & Wyss-Coray, T.
- ORCID
- Jones, Robert C.
- Karkanias, Jim
- Krasnow, Mark A.
- Pisco, Angela Oliveira
- Quake, Stephen R.
- Salzman, Julia
- Yosef, Nir
- Harper, William
- Salehi, Ahmad
- Aaron, Ksenia A.
- Concepcion, Waldo
- Gardner, James M.
- Kelly, Burnett
- Neidlinger, Nikole
- Wang, Zifa
- Morri, Maurizio
- Tan, Serena Y.
- Travaglini, Kyle J.
- Xu, Chenling
- Almanzar, Nicole
- Antony, Jane
- Beyersdorf, Benjamin
- Burhan, Deviana
- Carter, Matthew M.
- Chan, Charles K. F.
- Chang, Charles A.
- Chang, Stephen
- Colville, Alex
- Culver, Rebecca N.
- Cvijović, Ivana
- D’Amato, Gaetano
- Ezran, Camille
- Galdos, Francisco X.
- Gillich, Astrid
- Goodyer, William R.
- Hang, Yan
- Houshdaran, Sahar
- Huang, Xianxi
- Irwin, Juan C.
- Jang, SoRi
- Kershner, Aaron M.
- Kim, Soochi
- Kiss, Bernhard
- Kumar, Maya E.
- Kuo, Angera H.
- Leylek, Rebecca
- Li, Baoxiang
- Loeb, Gabriel B.
- Lu, Wan-Jin
- Mantri, Sruthi
- Markovic, Maxim
- McAlpine, Patrick L.
- Mrouj, Karim
- Mukherjee, Shravani
- Muser, Tyler
- Neuhöfer, Patrick
- Perez, Kimberly
- Phansalkar, Ragini
- Puluca, Nazan
- Qi, Zhen
- Raquer-McKay, Hayley
- Scott, Bronwyn
- Segal, Joe
- Sikandar, Shaheen
- Spencer, Sean P.
- Steffes, Lea C.
- Subramaniam, Varun R.
- Swarup, Aditi
- Swift, Michael
- Trimm, Emily
- Veizades, Stefan
- Vijayakumar, Sivakamasundari
- Vo, Kim Chi
- Vorperian, Sevahn K.
- Wang, Wanxin
- Weinstein, Hannah N. W.
- Winkler, Juliane
- Xie, Jamie
- Yung, Andrea R.
- Zhang, Yue
- Detweiler, Angela M.
- Mekonen, Honey
- Neff, Norma F.
- Tan, Michelle
- Bean, Gregory R.
- Charu, Vivek
- Forgó, Erna
- Martin, Brock A.
- Ozawa, Michael G.
- Silva, Oscar
- Toland, Angus
- Vemuri, Venkata N. P.
- Afik, Shaked
- Awayan, Kyle
- Botvinnik, Olga Borisovna
- Byrne, Ashley
- Dehghannasiri, Roozbeh
- Gayoso, Adam
- Granados, Alejandro A.
- Mahmoudabadi, Gita
- McGeever, Aaron
- Olivieri, Julia Eve
- Stanley, Geoff
- Tarashansky, Alexander J.
- Wang, Peter
- Wang, Sheng
- Xing, Galen
- Dethlefsen, Les
- Ho, Po-Yi
- Liu, Shixuan
- Maltzman, Jonathan S.
- Metzger, Ross J.
- Sinha, Rahul
- Song, Hanbing
- Wang, Bruce
- Artandi, Steven E.
- Beachy, Philip A.
- Clarke, Michael F.
- Giudice, Linda C.
- Huang, Franklin W.
- Huang, Kerwyn Casey
- Idoyaga, Juliana
- Kim, Seung K.
- Kuo, Christin S.
- Nguyen, Patricia
- Rando, Thomas A.
- Reiter, Jeremy
- Relman, David A.
- Sonnenburg, Justin L.
- Wu, Albert
- Wu, Sean M.
- Venue
- Science
- Published
- 2022-05-13
- Volume
- 376
- Issue
- 6594
- Pages
- eabl4896-eabl4896
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC9812260
- OpenAlex
- W4280598116
- Cited by
- 1,056
- References
- 17
- Citations by year
- 2026: 173 · 2025: 301 · 2024: 272 · 2023: 219 · 2022: 82 · 2021: 9
- FWCI
- 71.60
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Silicon Valley Community Foundation
- Chan Zuckerberg Initiative
- National Institutes of Health
- University of California, San Francisco (P30DK026743)
- National Heart, Lung, and Blood Institute (T32HL120824)
- National Institute on Deafness and Other Communication Disorders (R01DC016892)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK126482, R01DK128932, P30DK026743)
- Liver Center, University of California, San Francisco (P30 DK026743)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Human Reference Atlas, single-cell transcriptomics, cell types, tissue-specific gene expression, cell cycle, cell proliferation, RNA splicing
- MeSH terms
- Atlases as Topic, B-Lymphocytes, Cells, Humans, Organ Specificity, RNA Splicing, T-Lymphocytes, Single-Cell Analysis, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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