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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, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.ORCID iD: 0000-0001-8643-5846
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.ORCID iD: 0000-0001-8643-5846
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-7000-4416
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.ORCID iD: 0000-0002-2669-7796
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Number of Authors: 342025 (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]
Cell type classification, Gene expression mapping, Human Protein Atlas, Single-cell
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)
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URN: urn:nbn:se:kth:diva-366187DOI: 10.1186/s13059-025-03616-4ISI: 001502167900001PubMedID: 40462185Scopus ID: 2-s2.0-105007441526OAI: oai:DiVA.org:kth-366187DiVA, id: diva2:1981911
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Not duplicate with DiVA 1959447

QC 20250707

Available from: 2025-07-07 Created: 2025-07-07 Last updated: 2025-08-15Bibliographically approved

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Shi, MengnanShi, MengnanKarlsson, MaxAlvez, Maria BuenoJin, HanYuan, MengLi, XiangyuYang, HongSong, XiyaSjöstedt, EvelinaEdfors, FredrikOksvold, Pervon Feilitzen, KalleZwahlen, MartinForsberg, MattiasJohansson, FredricMardinoglu, AdilSivertsson, ÅsaFagerberg, LinnUhlén, MathiasZhang, Cheng

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Shi, MengnanShi, MengnanKarlsson, MaxAlvez, Maria BuenoJin, HanYuan, MengLi, XiangyuYang, HongSong, XiyaSjöstedt, EvelinaEdfors, FredrikOksvold, Pervon Feilitzen, KalleZwahlen, MartinForsberg, MattiasJohansson, FredricMardinoglu, AdilSivertsson, ÅsaFagerberg, LinnUhlén, MathiasZhang, Cheng
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Science for Life Laboratory, SciLifeLabSystems Biology
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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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