{"id":["DOI:10.1038/s41586-021-04158-y"],"title":["Single-cell transcriptomic characterization of a gastrulating human embryo"],"publication_date":["2021-11-17"],"authors":{"ORCID:0000-0001-7884-1756":{"id":["ORCID:0000-0001-7884-1756"],"family_name":["Tyser"],"personal_name":["Richard C. V."],"affiliations":{"ROR:052gg0110":{"organization_name":["University of Oxford"]}}},"ORCID:0000-0003-0008-1413":{"id":["ORCID:0000-0003-0008-1413"],"family_name":["Mahammadov"],"personal_name":["Elmir"],"affiliations":{"ROR:00cfam450":{"organization_name":["Helmholtz Zentrum München"]}}},"ORCID:0000-0002-9016-7992":{"id":["ORCID:0000-0002-9016-7992"],"family_name":["Nakanoh"],"personal_name":["Shota"],"affiliations":{"ROR:05nz0zp31":{"organization_name":["Wellcome/MRC Cambridge Stem Cell Institute"]}}},"ORCID:0000-0002-3848-2602":{"id":["ORCID:0000-0002-3848-2602"],"family_name":["Vallier"],"personal_name":["Ludovic"],"affiliations":{"ROR:0493xsw21":{"organization_name":["Berlin Institute of Health at Charité - Universitätsmedizin Berlin"]},"ROR:03ate3e03":{"organization_name":["Max Planck Institute for Molecular Genetics"]}}},"ORCID:0000-0002-4956-2843":{"id":["ORCID:0000-0002-4956-2843"],"family_name":["Scialdone"],"personal_name":["Antonio"],"affiliations":{"ROR:00cfam450":{"organization_name":["Helmholtz Zentrum München"]}}},"ORCID:0000-0001-5726-7791":{"id":["ORCID:0000-0001-5726-7791"],"family_name":["Srinivas"],"personal_name":["Shankar"],"affiliations":{"ROR:052gg0110":{"organization_name":["University of Oxford"]}},"HDBItheme":["Cardiopulmonary"]}},"abstract":["Gastrulation is the fundamental process in all multicellular animals through which the basic body plan is first laid down 1,2,3,4. It is pivotal in generating cellular diversity coordinated with spatial patterning. In humans, gastrulation occurs in the third week after fertilization. Our understanding of this process in humans is relatively limited and based primarily on historical specimens 5,6,7,8, experimental models 9,10,11,12 or, more recently, in vitro cultured samples 13,14,15,16. Here we characterize in a spatially resolved manner the single-cell transcriptional profile of an entire gastrulating human embryo, staged to be between 16 and 19 days after fertilization. We use these data to analyse the cell types present and to make comparisons with other model systems. In addition to pluripotent epiblast, we identified primordial germ cells, red blood cells and various mesodermal and endodermal cell types. This dataset offers a unique glimpse into a central but inaccessible stage of our development. This characterization provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro."],"datasets":{"ArrayExpress:E-MTAB-9388":{"id":["ArrayExpress:E-MTAB-9388"],"title":["A spatially resolved single cell atlas of human gastrulation"],"description":["Single-cell RNA-seq of 1195 cells obtained from a human embryo at embryonic day 16."],"authors":{"ORCID:0000-0003-0008-1413":{"id":["ORCID:0000-0003-0008-1413"],"family_name":["Mahammadov"],"personal_name":["Elmir"],"affiliations":{"ROR:00cfam450":{"organization_name":["Helmholtz Zentrum München"]}}}},"tags":["spatial","sequencing"]}},"code":{"SWHID:swh:1:dir:bf91de9471e0fb7d0d7c9b0de6e235a405d9718e":{"id":["SWHID:swh:1:dir:bf91de9471e0fb7d0d7c9b0de6e235a405d9718e"],"title":["Human gastrula single-cell data shiny app code and data."],"description":["raw_reads.rds is the gene expression matrix of raw unnormalized reads. umap.rds contains information about UMAP coordinates and cell type annotations of the cells. The order of the cells in raw_reads.rds and umap.rds files are the same.\nApp available at: https://www.human-gastrula.net"],"authors":{"ORCID:0000-0003-0008-1413":{"id":["ORCID:0000-0003-0008-1413"],"family_name":["Mahammadov"],"personal_name":["Elmir"],"affiliations":{"ROR:00cfam450":{"organization_name":["Helmholtz Zentrum München"]}}}}}},"HDBItheme":["Cardiopulmonary"]}