A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics
New technologies enable single-cell transcriptome analysis, mapping genome-wide expression across the human body. Here, we present an extended analysis of protein-coding genes in all major human tissues and organs, combining single-cell and bulk transcriptomics. To enhance transcriptome depth, 31 tissues were analyzed using a pooling method, identifying 557 unique cell clusters, manually annotated by marker gene expression. Genes were classified by body-wide expression and validated through antibody-based profiling. All results are available in the updated open-access Single Cell Type section of the Human Protein Atlas for genome-wide exploration of genes, proteins, and their spatial distribution in cells.
Authors
- Loren Méar (ORCID: https://orcid.org/0000-0001-9333-0110)
- Max Karlsson (ORCID: https://orcid.org/0000-0002-7000-4416)
- Fredrik Pontén (ORCID: https://orcid.org/0000-0003-0703-3940)
- Jan Mulder (ORCID: https://orcid.org/0000-0003-3717-5018)
- Fredrik Edfors (ORCID: https://orcid.org/0000-0002-0017-7987)
- Lynn M. Butler (ORCID: https://orcid.org/0000-0002-2352-8217)
- Linn Fagerberg (ORCID: https://orcid.org/0000-0003-0198-7137)
- Wen Zhong (ORCID: https://orcid.org/0000-0002-7422-6104)
- Cecilia Lindskog (ORCID: https://orcid.org/0000-0001-5611-1015)
- Adil Mardinoğlu (ORCID: https://orcid.org/0000-0002-4254-6090)
- Andreas Digre (ORCID: https://orcid.org/0000-0003-1145-6700)
- Fredric Johansson (ORCID: https://orcid.org/0000-0001-5160-9543)
- Xiya Song (ORCID: https://orcid.org/0009-0001-3893-682X)
- Yonglun Luo (ORCID: https://orcid.org/0000-0002-0007-7759)
- Per Oksvold (ORCID: https://orcid.org/0000-0003-3014-5502)
- Kalle von Feilitzen (ORCID: https://orcid.org/0000-0002-0257-7554)
- Hong Yang (ORCID: https://orcid.org/0009-0002-0414-2471)
- Martin Zwahlen (ORCID: https://orcid.org/0000-0002-0064-4776)
- Han Jin
- Mathias Uhlén (ORCID: https://orcid.org/0000-0002-4858-8056)
- Jimmy Vuu
- Cheng Zhang (ORCID: https://orcid.org/0000-0002-3721-8586)
- Borbala Katona (ORCID: https://orcid.org/0000-0003-2431-5288)
- Meng Yuan (ORCID: https://orcid.org/0000-0002-9248-3294)
- Emil Lindström
- Feria Hikmet (ORCID: https://orcid.org/0000-0002-3750-9308)
- Tomas Hökfelt
- Rutger Schutten (ORCID: https://orcid.org/0000-0001-8787-8868)
- Mengnan Shi (ORCID: https://orcid.org/0000-0001-8643-5846)
- Åsa Sivertsson (ORCID: https://orcid.org/0000-0001-8800-8469)
- María Bueno Álvez (ORCID: https://orcid.org/0000-0002-2669-7796)
- Evelina Sjöstedt (ORCID: https://orcid.org/0000-0002-0327-7377)
- Xiangyü Li (ORCID: https://orcid.org/0000-0002-8301-9959)
- Mattias Forsberg
Institutions
- Linköping University (SE)
- Uppsala University (SE)
- Steno Diabetes Centers (DK)
- Harvard University (US)
- Aarhus University (DK)
- Science for Life Laboratory (SE)
- Aarhus University Hospital (DK)
- Karolinska Institutet (SE)
- UiT The Arctic University of Norway (NO)
- KTH Royal Institute of Technology (SE)
Publication Details
- Journal
- Genome biology
- Published
- 2025-06-03
- DOI
- https://doi.org/10.1186/s13059-025-03616-4
- Citations
- 5
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 4.03
Funders
- Knut och Alice Wallenbergs Stiftelse
- Kungliga Tekniska Högskolan
- Vetenskapsrådet
- Science for Life Laboratory