{"id":["DOI:10.1126/science.add7564"],"title":["Yolk sac cell atlas reveals multiorgan functions during human early development"],"publication_date":["2023-08-18"],"authors":{"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:0000-0001-9595-4605":{"id":["ORCID:0000-0001-9595-4605"],"family_name":["Botting"],"personal_name":["Rachel A."],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0001-8494-8138":{"id":["ORCID:0000-0001-8494-8138"],"family_name":["Rose"],"personal_name":["Antony"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0003-3058-8952":{"id":["ORCID:0000-0003-3058-8952"],"family_name":["Webb"],"personal_name":["Simone"],"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:0000-0002-6808-6010":{"id":["ORCID:0000-0002-6808-6010"],"family_name":["Gitton"],"personal_name":["Yorick"],"affiliations":{"ROR:000zhpw23":{"organization_name":["Institut de la Vision"]}}},"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:0000-0003-2352-0773":{"id":["ORCID:0000-0003-2352-0773"],"family_name":["Quiroga Londoño"],"personal_name":["Mariana"],"affiliations":{"ROR:05nz0zp31":{"organization_name":["Wellcome/MRC Cambridge Stem Cell Institute"]}}},"AUTHTEMP:00020":{"id":["AUTHTEMP:00020"],"family_name":["Mather"],"personal_name":["Michael"],"affiliations":{"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0002-5078-2333":{"id":["ORCID:0000-0002-5078-2333"],"family_name":["Mende"],"personal_name":["Nicole"],"affiliations":{"ROR:05nz0zp31":{"organization_name":["Wellcome/MRC Cambridge Stem Cell Institute"]}}},"ORCID:0000-0001-5975-0138":{"id":["ORCID:0000-0001-5975-0138"],"family_name":["Imaz-Rosshandler"],"personal_name":["Ivan"],"affiliations":{"ROR:05nz0zp31":{"organization_name":["Wellcome/MRC Cambridge Stem Cell Institute"]},"ROR:00tw3jy02":{"organization_name":["MRC Laboratory of Molecular Biology"]}}},"ORCID:0000-0002-2694-1189":{"id":["ORCID:0000-0002-2694-1189"],"family_name":["Yang"],"personal_name":["Lu"],"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:0000-0003-3943-8424":{"id":["ORCID:0000-0003-3943-8424"],"family_name":["Basurto-Lozada"],"personal_name":["Daniela"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0002-8802-0473":{"id":["ORCID:0000-0002-8802-0473"],"family_name":["Chipampe"],"personal_name":["Nana-Jane"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0002-1225-0870":{"id":["ORCID:0000-0002-1225-0870"],"family_name":["Rook"],"personal_name":["Victoria"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0003-1208-8356":{"id":["ORCID:0000-0003-1208-8356"],"family_name":["Lee"],"personal_name":["Jimmy Tsz Hang"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}},"ORCID:0000-0001-6965-0528":{"id":["ORCID:0000-0001-6965-0528"],"family_name":["Ton"],"personal_name":["Mai-Linh"],"affiliations":{"ROR:05nz0zp31":{"organization_name":["Wellcome/MRC Cambridge Stem Cell Institute"]}}},"ORCID:0000-0002-6418-2849":{"id":["ORCID:0000-0002-6418-2849"],"family_name":["Keitley"],"personal_name":["Daniel"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:013meh722":{"organization_name":["University of Cambridge"]}}},"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:0000-0002-5559-9394":{"id":["ORCID:0000-0002-5559-9394"],"family_name":["Vijayabaskar"],"personal_name":["M. 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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"]}},"abstract":["The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference of the human YS from 3 to 8 postconception weeks by integrating single-cell protein and gene expression data. Beyond its recognized role as a site of hematopoiesis, we highlight roles in metabolism, coagulation, vascular development, and hematopoietic regulation. We reconstructed the emergence and decline of YS hematopoietic stem and progenitor cells from hemogenic endothelium and revealed a YS-specific accelerated route to macrophage production that seeds developing organs. The multiorgan functions of the YS are superseded as intraembryonic organs develop, effecting a multifaceted relay of vital functions as pregnancy proceeds."],"HDBItheme":["BloodAndImmune"],"datasets":{"BioStudies:S-DHCA0":{"id":["BioStudies:S-DHCA0"],"title":["Yolk sac cell atlas reveals multiorgan functions during human early development"],"description":["The yolk sac (YS) represents an evolutionarily-conserved extra-embryonic structure that ensures timely delivery of nutritional support and oxygen to the developing embryo.  However, the YS remains ill-defined in humans. We therefore assemble a complete single cell 3D map of human YS from 3-8 post conception weeks by integrating multiomic protein and gene expression data. We reveal the YS as a site of primitive and definitive haematopoiesis including a YS-specific accelerated route to macrophage production, a source of nutritional/metabolic support and a regulator of oxygen-carrying capacity. We reconstruct the emergence of primitive haematopoietic stem and progenitor cells from YS hemogenic endothelium and their decline upon stromal support modulation as intraembryonic organs specialise to assume these functions. The YS therefore functions as ‘three organs in one’ revealing a multifaceted relay of vital organismal functions as pregnancy proceeds.\nWe provide a range of multi-modal spatially-defined validation imaging data including hiplex_RNA-scope, Light-sheet-microscopy and Immunofluorescence data.\nData type: - hiplex_RNA-scope - Immunofluorescence - Light-sheet-microscopy (not on farm)"],"authors":{"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:0000-0002-4201-9215":{"id":["ORCID:0000-0002-4201-9215"],"family_name":["Inoue"],"personal_name":["Megumi"],"affiliations":{"ROR:000zhpw23":{"organization_name":["Institut de la Vision"]}},"HDBItheme":["BloodAndImmune"]},"ORCID:0000-0001-9595-4605":{"id":["ORCID:0000-0001-9595-4605"],"family_name":["Botting"],"personal_name":["Rachel A."],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"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":["imaging","spatial"]},"URL:https://developmental.cellatlas.io/yolk-sac":{"id":["URL:https://developmental.cellatlas.io/yolk-sac"],"title":["Developmental Cell Atlas: Yolk sac cell atlas reveals multiorgan functions during human early development"],"description":["This study generated a multi-omic atlas of the human yolk sac (3–8 weeks post-conception) using single-cell gene/protein data. It revealed that the yolk sac not only supports early haematopoiesis but also contributes to metabolism, coagulation and vascular development, and seeds macrophages into organs via an accelerated pathway. "],"authors":{"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:0000-0001-9595-4605":{"id":["ORCID:0000-0001-9595-4605"],"family_name":["Botting"],"personal_name":["Rachel A."],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}}},"tags":["imaging","spatial","sequencing"]}},"code":{"SWHID:swh:1:dir:1c585acedaa8855cc6a7d0f5ba535667e71c9df4":{"id":["SWHID:swh:1:dir:1c585acedaa8855cc6a7d0f5ba535667e71c9df4"],"title":["FCA Human Yolksac study"],"description":["In this study, we profile in detail the human yolk sac (YS) from 3-8 post-conception weeks (~169k cells) and matched embryonic liver using scRNA-seq, CITE-seq, spatial validation using RNAscope and tissue context of near whole YS using 3D light sheet microscopy. We contextualised human YS haematopoiesis and metabolic functions through comparison with datasets from matched embryonic liver, human and mouse gastrulas, fetal bone marrow, embryonic skin and brain and inducible pluripotent stem cell-derived myeloid cells."],"authors":{"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:0000-0001-8494-8138":{"id":["ORCID:0000-0001-8494-8138"],"family_name":["Rose"],"personal_name":["Antony"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0003-3058-8952":{"id":["ORCID:0000-0003-3058-8952"],"family_name":["Webb"],"personal_name":["Simone"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:01kj2bm70":{"organization_name":["Newcastle University"]}}},"ORCID:0000-0003-2352-0773":{"id":["ORCID:0000-0003-2352-0773"],"family_name":["Quiroga Londoño"],"personal_name":["Mariana"],"affiliations":{"ROR:05nz0zp31":{"organization_name":["Wellcome/MRC Cambridge Stem Cell Institute"]}}}}}}}