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A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics
KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer precision medicine. Karolinska Inst, Dept Clin Sci Intervent & Technol, Div Obstet & Gynecol, S-14186 Stockholm, Sweden..
KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
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2025 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 26, no 1, article id 152Article in journal (Refereed) Published
Abstract [en]

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.
Place, publisher, year, edition, pages
Springer Nature, 2025. Vol. 26, no 1, article id 152
Keywords [en]
Single-cell, Gene expression mapping, Cell type classification, Human Protein Atlas
National Category
Bioinformatics and Computational Biology Cell and Molecular Biology Medical Genetics and Genomics Medical Biotechnology (Focus on Cell Biology, (incl. Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
URN: urn:nbn:se:uu:diva-561490DOI: 10.1186/s13059-025-03616-4ISI: 001502167900001PubMedID: 40462185Scopus ID: 2-s2.0-105007441526OAI: oai:DiVA.org:uu-561490DiVA, id: diva2:1975816
Funder
Knut and Alice Wallenberg Foundation, 2022-06725Swedish Research CouncilAvailable from: 2025-06-24 Created: 2025-06-24 Last updated: 2025-06-24Bibliographically approved

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Méar, LorenDigre, AndreasSchutten, RutgerKatona, BorbalaVuu, JimmyHikmet Noraddin, FeriaPontén, FredrikLindskog, Cecilia

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Méar, LorenDigre, AndreasSchutten, RutgerKatona, BorbalaVuu, JimmyHikmet Noraddin, FeriaPontén, FredrikLindskog, Cecilia
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Cancer precision medicineDepartment of Immunology, Genetics and Pathology
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Genome Biology
Bioinformatics and Computational BiologyCell and Molecular BiologyMedical Genetics and GenomicsMedical Biotechnology (Focus on Cell Biology, (incl. Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)

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