ArticleScience (New York, N.Y.)2022
Cross-tissue immune cell analysis reveals tissue-specific features in humans.
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Article in Science (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 721 papers.
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721citing papers in PubMed
86.5field-weighted citation impact, top 1% of its field
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721 citing papers in PubMed, 1,068 citations in OpenAlex.
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- Spatial biology reveals altered macrophage states in immunosuppressed non-melanoma skin cancer.Cell · 2026Article
- A Gene-Program Architecture of Mouse T cells.bioRxiv : the preprint server for biology · 2026Article
- Flow Orchestrated Regulatory Genomics Engine (FORGE): A Configurable Nextflow Pipeline for End-to-End snMultiome Analysis.bioRxiv : the preprint server for biology · 2026Article
661 more citing papers are in PubMed but not listed here.
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Authors and funding
41 authors at 7 institutions in 2 countries.
C Domínguez Conde *Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-8684-4655
C Xu *Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-6265-999X
L B Jarvis *Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.ORCID 0000-0002-5760-0125
D B Rainbow *Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.ORCID 0000-0003-4931-3289
S B Wells *Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID 0000-0001-5428-0683
T GomesWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0003-1333-0191
S K HowlettDepartment of Clinical Neurosciences, University of Cambridge, Cambridge, UK.ORCID 0000-0003-0504-4937
O SuchanekMolecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
K PolanskiWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-2586-9576
H W KingCentre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK.ORCID 0000-0001-5972-8926
L MamanovaWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0003-1463-8622
N HuangWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0001-8849-038X
P A SzaboDepartment of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.ORCID 0000-0003-1603-761X
L RichardsonWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0001-9064-1271
L BoltWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0001-7293-0774
E S FasouliWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0003-1621-3396
K T MahbubaniDepartment of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.ORCID 0000-0002-1327-2334
M PreteWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-5946-821X
L TuckWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-1837-7549
N RichozMolecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
Z K TuongWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-6735-6808
L CamposWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0003-2445-7120
H S MousaDepartment of Clinical Neurosciences, University of Cambridge, Cambridge, UK.ORCID 0000-0002-8327-7114
E J NeedhamDepartment of Clinical Neurosciences, University of Cambridge, Cambridge, UK.ORCID 0000-0001-7042-7462
S PritchardWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
T LiWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-8240-4476
R ElmentaiteWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0001-7366-5466
J ParkWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-1687-2423
E RahmaniCenter for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
D ChenDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID 0000-0002-9710-1857
D K MenonDepartment of Anaesthesia, University of Cambridge, Cambridge, UK.ORCID 0000-0002-3228-9692
O A BayraktarWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
L K JamesCentre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK.ORCID 0000-0002-2252-4636
K B MeyerWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0001-5906-1498
N YosefCenter for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.ORCID 0000-0001-9004-1225
M R ClatworthyWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-3340-9828
P A SimsDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID 0000-0002-3921-4837
D L FarberDepartment of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.ORCID 0000-0001-8236-9183
K Saeb-Parsy *Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.ORCID 0000-0002-0633-3696
J L Jones *Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.ORCID 0000-0003-4974-1371
S A Teichmann *Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID 0000-0002-6294-6366
Wellcome Sanger Institute · GBUniversity of Cambridge · GBColumbia University Irving Medical Center · USQueen Mary University of London · GBRagon Institute of MGH, MIT and Harvard · USUniversity of California, Berkeley · USWest Suffolk NHS Foundation Trust · GB
Funding
Transcriptomics and Repertoire ProfilingP01AI106697 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Donna L. Farber · 2013 to 2026
$31.3MViral Assays CoreU19AI128949 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Donna L. Farber, Peter Alan Sims · 2017 to 2026
$26.4MThe Organoid and Cell Culture CoreP30DK132710 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Robert F. Schwabe · 2022 to 2026
$7.2MImmunobiology and alveolar physiology of the aging lungU01HL145547 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BHATTACHARYA, JAHAR, FARBER, DONNA L. · 2019 to 2022
$2.6MImpact of CD8+ T cell functionality on HIV viral escapeK22AI066976 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI BETTS, MICHAEL R · 2005 to 2006
$270kCancer Research UK 10208European Research Council 646794NHLBI NIH HHS U01 HL145547NIAID NIH HHS K22 AI066976NIAID NIH HHS P01 AI106697NIAID NIH HHS U19 AI128949NIDDK NIH HHS P30 DK132710Wellcome Trust 105924Wellcome Trust 206194
Abstract
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.
Indexed as
B-LymphocytesMachine LearningSequence Analysis, RNASingle-Cell AnalysisT-LymphocytesTranscriptomeCells, CulturedHumansOrgan Specificity
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.