A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics.

Shi M, Méar L, Karlsson M, Álvez MB, Digre A, Schutten R, Katona B, Vuu J, Lindström E, Hikmet F, Jin H, Yuan M, Li X, Yang H, Song X, Sjöstedt E, Edfors F, Oksvold P, von Feilitzen K, Zwahlen M, Forsberg M, Johansson F, Mulder J, Hökfelt T, Luo Y, Butler L, Zhong W, Mardinoglu A, Sivertsson Å, Ponten F, Fagerberg L, Lindskog C, Uhlén M, Zhang C

Genome Biol. 26 (1) 152 [2025-06-03; online 2025-06-03]

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.

PubMed 40462185

DOI 10.1186/s13059-025-03616-4

Crossref 10.1186/s13059-025-03616-4

pmc: PMC12131445
pii: 10.1186/s13059-025-03616-4