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A lineage-resolved molecular atlas of C. elegans 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
doi: https://doi.org/10.1101/565549
Jonathan S. Packer
University of Washington;
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  • For correspondence: jspacker@uw.edu
Qin Zhu
University of Pennsylvania
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Chau Huynh
University of Washington;
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Priya Sivaramakrishnan
University of Pennsylvania
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Elicia Preston
University of Pennsylvania
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Hannah Dueck
University of Pennsylvania
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Derek Stefanik
University of Pennsylvania
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Kai Tan
University of Pennsylvania
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Cole Trapnell
University of Washington;
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Junhyong Kim
University of Pennsylvania
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  • For correspondence: junhyong@sas.upenn.edu
Robert H. Waterston
University of Washington;
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  • For correspondence: watersto@uw.edu
John I. Murray
University of Pennsylvania
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  • For correspondence: jmurr@pennmedicine.upenn.edu
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Abstract

C. elegans is an animal with few cells, but a striking diversity of cell types. Here, we characterize the molecular basis for their specification by profiling the transcriptomes of 84,625 single embryonic cells. We identify 284 terminal and pre-terminal cell types, mapping most single cell transcriptomes to their exact position in the invariant C. elegans lineage. We use these annotations to perform the first quantitative analysis of the relationship between lineage and the transcriptome for a whole organism. We find that a strong lineage-transcriptome correlation in the early embryo breaks down in the final two cell divisions as cells adopt their terminal fates and that most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state. Users can explore our data with a graphical application VisCello.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted March 01, 2019.
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A lineage-resolved molecular atlas of C. elegans 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
bioRxiv 565549; doi: https://doi.org/10.1101/565549
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A lineage-resolved molecular atlas of C. elegans 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
bioRxiv 565549; doi: https://doi.org/10.1101/565549

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