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Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types

View ORCID ProfileTara Chari, View ORCID ProfileBrandon Weissbourd, View ORCID ProfileJase Gehring, View ORCID ProfileAnna Ferraioli, View ORCID ProfileLucas Leclère, View ORCID ProfileMakenna Herl, Fan Gao, View ORCID ProfileSandra Chevalier, View ORCID ProfileRichard R. Copley, Evelyn Houliston, David J. Anderson, View ORCID ProfileLior Pachter
doi: https://doi.org/10.1101/2021.01.22.427844
Tara Chari
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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Brandon Weissbourd
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
2Tianqiao and Chrissy Chen Institute for Neuroscience, Pasadena, CA 91125
3Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
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Jase Gehring
4Department of Genome Sciences, University of Washington, Seattle, Washington 98195
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Anna Ferraioli
5Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 France
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Lucas Leclère
5Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 France
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Makenna Herl
6University of New Hampshire School of Law, Concord, New Hampshire, 03301
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Fan Gao
7Caltech Bioinformatics Resource Center, California Institute of Technology, Pasadena, CA 91125
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Sandra Chevalier
5Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 France
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Richard R. Copley
5Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 France
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  • ORCID record for Richard R. Copley
  • For correspondence: lpachter@caltech.edu
Evelyn Houliston
5Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 France
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  • For correspondence: lpachter@caltech.edu
David J. Anderson
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
2Tianqiao and Chrissy Chen Institute for Neuroscience, Pasadena, CA 91125
3Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
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  • For correspondence: lpachter@caltech.edu
Lior Pachter
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
8Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125
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  • ORCID record for Lior Pachter
  • For correspondence: lpachter@caltech.edu
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Abstract

We present an organism-wide, transcriptomic cell atlas of the hydrozoan medusa Clytia hemisphaerica, and determine how its component cell types respond to starvation. Utilizing multiplexed scRNA-seq, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run, we avoid artifacts from batch effects and are able to discern shifts in cell state in response to organismal perturbations. This work serves as a foundation for future studies of development, function, and plasticity in a genetically tractable jellyfish species. Moreover, we introduce a powerful workflow for high-resolution, whole animal, multiplexed single-cell genomics (WHAM-seq) that is readily adaptable to other traditional or non-traditional model organisms.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Grammatical text edits; Figure 2 revised; Supplemental files (methods) updated;

  • https://github.com/pachterlab/CWGFLHGCCHAP_2021

  • https://pachterlab.github.io/CWGFLHGCCHAP_2021/

  • https://data.caltech.edu/

Copyright 
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-NC 4.0 International license.
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Posted February 07, 2021.
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Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types
Tara Chari, Brandon Weissbourd, Jase Gehring, Anna Ferraioli, Lucas Leclère, Makenna Herl, Fan Gao, Sandra Chevalier, Richard R. Copley, Evelyn Houliston, David J. Anderson, Lior Pachter
bioRxiv 2021.01.22.427844; doi: https://doi.org/10.1101/2021.01.22.427844
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Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types
Tara Chari, Brandon Weissbourd, Jase Gehring, Anna Ferraioli, Lucas Leclère, Makenna Herl, Fan Gao, Sandra Chevalier, Richard R. Copley, Evelyn Houliston, David J. Anderson, Lior Pachter
bioRxiv 2021.01.22.427844; doi: https://doi.org/10.1101/2021.01.22.427844

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