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

Chari, Tara and Weissbourd, Brandon and Gehring, Jase and Ferraioli, Anna and Leclère, Lucas and Herl, Makenna and Gao, Fan and Chevalier, Sandra and Copley, Richard R. and Houliston, Evelyn and Anderson, David J. and Pachter, Lior (2021) Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types. . (Unpublished)

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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.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper ItemData
Chari, Tara0000-0002-6953-4313
Weissbourd, Brandon0000-0001-5422-3873
Gehring, Jase0000-0002-3894-9495
Ferraioli, Anna0000-0003-1817-6891
Leclère, Lucas0000-0002-7440-0467
Herl, Makenna0000-0001-8518-5179
Chevalier, Sandra0000-0002-2717-6925
Copley, Richard R.0000-0001-7846-4954
Anderson, David J.0000-0001-6175-3872
Pachter, Lior0000-0002-9164-6231
Additional Information: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. Version 1 - January 23, 2021; Version 2 - February 7, 2021. We thank Xiaolin Da and Xiao Wang for their technical assistance, Tsuyoshi Momose for his assistance with the single-cell experimentation, the Caltech Single-Cell Profiling and Engineering Center for use of their single-cell and sequencing tools, and the Caltech Bioinformatics Resource Center for transcriptome assembly and annotation analysis. We thank A. Sina Booeshaghi for help with kallisto, bustools, the kITE demultiplexing of the ClickTag reads, and for rescuing the stimulation experiment sequencing data. We thank Jocelyn Malamy for helping to establish Clytia work at Caltech. We thank Sophie Peron for initial characterization of some of the cell type marker genes, Pascal Lapébie for identification of novel neuropeptide sequences, and Muriel Jager for valuable advice on the in situ protocol. J.G., M.H. and L.P. were supported in part by a seed grant from the Chen Institute at the California Institute of Technology. T.C., J.G. and L.P. were supported in part by NIH U19MH114830 and NIH RF1AG062324A. We thank the Marine Resources Centre (CRBM and PIV imaging platform) of Institut de la Mer de Villefranche (IMEV), supported by EMBRC-France. The French state funds of EMBRC-France are managed by the ANR within the investments of the Future program. L.L. was supported by the Agence Nationale de la Recherche (ANR-19-CE13-0003) A.F., R.R.C, and E.H., were supported by the H2020 / Marie Skłodowska-Curie ITN "EvoCell" Grant agreement N° 766053. B.W. was supported in part by a Howard Hughes Medical Institute Fellowship of the Life Sciences Research Foundation and in part by NIH K99NS119749. This work was in part supported by the Whitman Center of the Marine Biological Laboratory in Woods Hole, MA, and a visiting grant from EMBRC-France. D.J.A. is an Investigator of the Howard Hughes Medical Institute. Code Availability: All code is available at The repository contains Google Colab notebooks that generate all the analyses and figures in the paper. The notebooks, which include the complete pre-processing of the raw data, provide a transparent implementation of the methods, and can be run for free in the Google cloud. Author Contributions: T.C., B.W., J.G., R.R.C., E.H., D.J.A, and L.P. conceived the experiments. J.G. and M.H. developed cell dissociation, fixation, and labeling procedures compatible with the 10X Genomics platform. T.C., B.W., and J.G. performed the single-cell experiments. B.W., A.F., L.L., and S.C. performed the in situ hybridization and other microscopy experiments. F.G and R.R.C. performed bioinformatics analysis including assembly and annotation of the transcriptome. T.C. and J.G. wrote scripts for processing the data and code for the analysis. T.C. developed the Google Colab notebooks. T.C., B.W., J.G., A.F., L.L.,R.C., E.H., D.J.A, and L.P. analyzed and interpreted the data. T.C., B.W., J.G., A.F., L.L., R.R.C., E.H., D.J.A, and L.P. contributed to writing and editing the manuscript. Competing Interests statement: The authors declare no competing interests.
Group:Tianqiao and Chrissy Chen Institute for Neuroscience
Funding AgencyGrant Number
Tianqiao and Chrissy Chen Institute for NeuroscienceUNSPECIFIED
Institut de la Mer de VillefrancheUNSPECIFIED
European Marine Biological Resource CentreUNSPECIFIED
Agence Nationale pour la Recherche (ANR)ANR-19-CE13-0003
Marie Curie Fellowship766053
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Woods Hole Oceanographic InstitutionUNSPECIFIED
Record Number:CaltechAUTHORS:20210126-133110736
Persistent URL:
Official Citation: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:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:107730
Deposited By: Tony Diaz
Deposited On:26 Jan 2021 21:51
Last Modified:08 Feb 2021 21:43

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