{"id":["DOI:10.1126/science.abo0510"],"title":["Mapping the developing human immune system across organs"],"publication_date":["2022-05-12"],"authors":{"ORCID:0000-0002-8813-0875":{"id":["ORCID:0000-0002-8813-0875"],"family_name":["Suo"],"personal_name":["Chenqu"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-7400-7438":{"id":["ORCID:0000-0002-7400-7438"],"family_name":["Dann"],"personal_name":["Emma"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-6397-3518":{"id":["ORCID:0000-0002-6397-3518"],"family_name":["Goh"],"personal_name":["Issac"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0003-4495-8205":{"id":["ORCID:0000-0003-4495-8205"],"family_name":["Jardine"],"personal_name":["Laura"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger 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University"]}}},"ORCID:0000-0002-4244-4019":{"id":["ORCID:0000-0002-4244-4019"],"family_name":["Stephenson"],"personal_name":["Emily"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0002-4255-9668":{"id":["ORCID:0000-0002-4255-9668"],"family_name":["Engelbert"],"personal_name":["Justin"],"affiliations":{"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0002-6735-6808":{"id":["ORCID:0000-0002-6735-6808"],"family_name":["Tuong"],"personal_name":["Zewen Kelvin"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:013meh722":{"organization_name":["University of Cambridge"]}}},"ORCID:0000-0002-2586-9576":{"id":["ORCID:0000-0002-2586-9576"],"family_name":["Polański"],"personal_name":["Krzysztof"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger 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Conde"],"personal_name":["Cecilia"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-2457-3554":{"id":["ORCID:0000-0002-2457-3554"],"family_name":["He"],"personal_name":["Peng"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:02catss52":{"organization_name":["European Bioinformatics Institute"]},"ROR:043mz5j54":{"organization_name":["University of California, San Francisco"]}}},"ORCID:0000-0001-5580-4848":{"id":["ORCID:0000-0001-5580-4848"],"family_name":["Pritchard"],"personal_name":["Sophie"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0001-5617-5350":{"id":["ORCID:0000-0001-5617-5350"],"family_name":["Miah"],"personal_name":["Mohi"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0001-5021-6473":{"id":["ORCID:0000-0001-5021-6473"],"family_name":["Moldovan"],"personal_name":["Corina"],"affiliations":{"ROR:05p40t847":{"organization_name":["Newcastle upon Tyne Hospitals NHS Foundation Trust"]}}},"ORCID:0000-0002-7162-7279":{"id":["ORCID:0000-0002-7162-7279"],"family_name":["Steemers"],"personal_name":["Alexander S."],"affiliations":{"ROR:05p40t847":{"organization_name":["Newcastle upon Tyne Hospitals NHS Foundation Trust"]}}},"ORCID:0000-0001-9268-3352":{"id":["ORCID:0000-0001-9268-3352"],"family_name":["Mazin"],"personal_name":["Pavel"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-5946-821X":{"id":["ORCID:0000-0002-5946-821X"],"family_name":["Prete"],"personal_name":["Martin"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-8086-812X":{"id":["ORCID:0000-0002-8086-812X"],"family_name":["Horsfall"],"personal_name":["Dave"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0001-9092-0852":{"id":["ORCID:0000-0001-9092-0852"],"family_name":["Marioni"],"personal_name":["John"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:02catss52":{"organization_name":["European Bioinformatics Institute"]},"ROR:0068m0j38":{"organization_name":["Cancer Research UK Cambridge Center"]}}},"ORCID:0000-0002-3340-9828":{"id":["ORCID:0000-0002-3340-9828"],"family_name":["Clatworthy"],"personal_name":["Menna R."],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:013meh722":{"organization_name":["University of Cambridge"]}}},"ORCID:0000-0002-3927-2084":{"id":["ORCID:0000-0002-3927-2084"],"family_name":["Haniffa"],"personal_name":["Muzlifah"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]},"ROR:05p40t847":{"organization_name":["Newcastle upon Tyne Hospitals NHS Foundation Trust"]},"ROR:0187kwz08":{"organization_name":["National Institute for Health Research"]}},"HDBItheme":["BloodAndImmune"]},"ORCID:0000-0002-6294-6366":{"id":["ORCID:0000-0002-6294-6366"],"family_name":["Teichmann"],"personal_name":["Sarah A."],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:013meh722":{"organization_name":["University of Cambridge"]}}}},"abstract":["Single-cell genomics studies have decoded the immune cell composition of several human prenatal organs but were limited in describing the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics to reconstruct the developing human immune system. This revealed the late acquisition of immune-effector functions by myeloid and lymphoid cell subsets and the maturation of monocytes and T cells before peripheral tissue seeding. Moreover, we uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine, and disease understanding."],"HDBItheme":["BloodAndImmune"],"datasets":{"ArrayExpress:E-MTAB-11343":{"id":["ArrayExpress:E-MTAB-11343"],"title":["Mapping the developing human immune system across organs - scRNA-seq"],"description":["We profiled hematopoietic, lymphoid and peripheral fetal organs to systematically assess the heterogeneity of immune cell populations across human tissues during development. Single-cell suspensions were obtained from fresh tissue. Cells were either DAPI-CD45+ or DAPI-CD45- FACS-isolated cells, or unsorted."],"authors":{"ORCID:0000-0002-7400-7438":{"id":["ORCID:0000-0002-7400-7438"],"family_name":["Dann"],"personal_name":["Emma"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-8813-0875":{"id":["ORCID:0000-0002-8813-0875"],"family_name":["Suo"],"personal_name":["Chenqu"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-3927-2084":{"id":["ORCID:0000-0002-3927-2084"],"family_name":["Haniffa"],"personal_name":["Muzlifah"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]},"ROR:05p40t847":{"organization_name":["Newcastle upon Tyne Hospitals NHS Foundation Trust"]},"ROR:0187kwz08":{"organization_name":["National Institute for Health Research"]}},"HDBItheme":["BloodAndImmune"]},"ORCID:0000-0002-6294-6366":{"id":["ORCID:0000-0002-6294-6366"],"family_name":["Teichmann"],"personal_name":["Sarah A."],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:013meh722":{"organization_name":["University of Cambridge"]}}}},"tags":["sequencing"]},"ArrayExpress:E-MTAB-11388":{"id":["ArrayExpress:E-MTAB-11388"],"title":["Mapping the developing human immune system across organs - VDJ-seq"],"description":["We profiled hematopoietic, lymphoid and peripheral fetal organs to systematically assess the heterogeneity of antigen receptors in immune cell populations across human tissues during development. Single-cell suspensions were obtained from fresh tissue. Cells were either DAPI-CD45+ or DAPI-CD45- FACS-isolated cells, or unsorted."],"authors":{"ORCID:0000-0002-7400-7438":{"id":["ORCID:0000-0002-7400-7438"],"family_name":["Dann"],"personal_name":["Emma"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-8813-0875":{"id":["ORCID:0000-0002-8813-0875"],"family_name":["Suo"],"personal_name":["Chenqu"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-6294-6366":{"id":["ORCID:0000-0002-6294-6366"],"family_name":["Teichmann"],"personal_name":["Sarah A."],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:013meh722":{"organization_name":["University of Cambridge"]}}},"ORCID:0000-0002-3927-2084":{"id":["ORCID:0000-0002-3927-2084"],"family_name":["Haniffa"],"personal_name":["Muzlifah"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]},"ROR:05p40t847":{"organization_name":["Newcastle upon Tyne Hospitals NHS Foundation Trust"]},"ROR:0187kwz08":{"organization_name":["National Institute for Health Research"]}},"HDBItheme":["BloodAndImmune"]}},"tags":["sequencing"]},"ArrayExpress:E-MTAB-11341":{"id":["ArrayExpress:E-MTAB-11341"],"title":["Mapping immune development across tissues in the human fetus - 10X spatial transcriptomics"],"description":["To study the spatial localisations of the cell populations in an early haematopoietic tissue and lymphoid organs critical for T and B cell development, we profiled fetal liver, thymus and spleen from 3 donors at 18 PCW with  sequencing-based spatial transcriptomics (10x Genomics Visium)."],"authors":{"ORCID:0000-0002-3927-2084":{"id":["ORCID:0000-0002-3927-2084"],"family_name":["Haniffa"],"personal_name":["Muzlifah"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]},"ROR:05p40t847":{"organization_name":["Newcastle upon Tyne Hospitals NHS Foundation Trust"]},"ROR:0187kwz08":{"organization_name":["National Institute for Health Research"]}},"HDBItheme":["BloodAndImmune"]},"ORCID:0000-0002-6294-6366":{"id":["ORCID:0000-0002-6294-6366"],"family_name":["Teichmann"],"personal_name":["Sarah A."],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:013meh722":{"organization_name":["University of Cambridge"]}}},"ORCID:0000-0002-7400-7438":{"id":["ORCID:0000-0002-7400-7438"],"family_name":["Dann"],"personal_name":["Emma"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-8813-0875":{"id":["ORCID:0000-0002-8813-0875"],"family_name":["Suo"],"personal_name":["Chenqu"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}}},"tags":["sequencing"]},"BioStudies:S-BIAD515":{"id":["BioStudies:S-BIAD515"],"title":["RNAScope Data - Mapping the developing human immune system across organs"],"description":["7 RNA images from 3 donors with either 3 or 4 plex RNAscope panel plus nuclear staining, see tsv file for metadata and pointer to relevant figure in the manuscript"],"authors":{"ORCID:0000-0002-8813-0875":{"id":["ORCID:0000-0002-8813-0875"],"family_name":["Suo"],"personal_name":["Chenqu"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-7400-7438":{"id":["ORCID:0000-0002-7400-7438"],"family_name":["Dann"],"personal_name":["Emma"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-7034-0524":{"id":["ORCID:0000-0002-7034-0524"],"family_name":["Yayon"],"personal_name":["Nadav"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:02catss52":{"organization_name":["European Bioinformatics Institute"]}}}},"tags":["imaging"]}},"code":{"DOI:10.5281/zenodo.6481461":{"id":["DOI:10.5281/zenodo.6481461"],"title":["Mapping the developing human immune system across organs"],"description":["Data processing and analysis scripts for fetal immune atlas"],"authors":{"ORCID:0000-0002-7400-7438":{"id":["ORCID:0000-0002-7400-7438"],"family_name":["Dann"],"personal_name":["Emma"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-8813-0875":{"id":["ORCID:0000-0002-8813-0875"],"family_name":["Suo"],"personal_name":["Chenqu"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-6397-3518":{"id":["ORCID:0000-0002-6397-3518"],"family_name":["Goh"],"personal_name":["Issac"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0001-9110-7441":{"id":["ORCID:0000-0001-9110-7441"],"family_name":["Kleshchevnikov"],"personal_name":["Vitalii"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}}}}}}