A lineage-resolved molecular atlas of embryogenesis at single-cell resolution.
Jonathan S Packer, Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim, Robert H Waterston, John I Murray
Author Information
Jonathan S Packer: Department of Genome Sciences, University of Washington, Seattle, WA, USA. ORCID
Qin Zhu: Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA. ORCID
Chau Huynh: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Priya Sivaramakrishnan: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. ORCID
Elicia Preston: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. ORCID
Hannah Dueck: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. ORCID
Derek Stefanik: Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. ORCID
Kai Tan: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. ORCID
Cole Trapnell: Department of Genome Sciences, University of Washington, Seattle, WA, USA. ORCID
Junhyong Kim: Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. junhyong@sas.upenn.edu watersto@uw.edu jmurr@pennmedicine.upenn.edu. ORCID
Robert H Waterston: Department of Genome Sciences, University of Washington, Seattle, WA, USA. junhyong@sas.upenn.edu watersto@uw.edu jmurr@pennmedicine.upenn.edu. ORCID
John I Murray: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. junhyong@sas.upenn.edu watersto@uw.edu jmurr@pennmedicine.upenn.edu. ORCID
is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and preterminal cell types, mapping most single-cell transcriptomes to their exact position in ' invariant lineage. Using these annotations, we find that (i) the correlation between a cell's lineage and its transcriptome increases from middle to late gastrulation, then falls substantially as cells in the nervous system and pharynx adopt their terminal fates; (ii) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and (iii) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.
