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Whole-body integration of gene expression and single-cell morphology

View ORCID ProfileHernando M. Vergara, View ORCID ProfileConstantin Pape, View ORCID ProfileKimberly I. Meechan, View ORCID ProfileValentyna Zinchenko, View ORCID ProfileChristel Genoud, View ORCID ProfileAdrian A. Wanner, View ORCID ProfileBenjamin Titze, View ORCID ProfileRachel M. Templin, View ORCID ProfilePaola Y. Bertucci, View ORCID ProfileOleg Simakov, View ORCID ProfilePedro Machado, View ORCID ProfileEmily L. Savage, View ORCID ProfileYannick Schwab, View ORCID ProfileRainer W. Friedrich, View ORCID ProfileAnna Kreshuk, Christian Tischer, View ORCID ProfileDetlev Arendt
doi: https://doi.org/10.1101/2020.02.26.961037
Hernando M. Vergara
1Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
2Sainsbury Wellcome Centre for Neural Circuits and Behaviour, Howland Street 25, London, W1T 4JG, UK
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Constantin Pape
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
4Heidelberg Collaboratory for Image Processing, Institut für Wissenschaftliches Rechnen, Ruprecht Karls Universität Heidelberg, Heidelberg
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Kimberly I. Meechan
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Valentyna Zinchenko
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Christel Genoud
5Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, 4058, Switzerland
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Adrian A. Wanner
5Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, 4058, Switzerland
6Princeton Neuroscience Institute, Princeton University, Washington Rd, Princeton, NJ, 08544, USA
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Benjamin Titze
5Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, 4058, Switzerland
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Rachel M. Templin
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Paola Y. Bertucci
1Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Oleg Simakov
7Department of Neuroscience and Developmental Biology, University of Vienna, Althanstr. 14, Vienna, 1090, Austria
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Pedro Machado
8Centre for Ultrastructural Imaging, King’s College London, New Hunt’s House Guy’s Campus, London, SE1 1UL, UK
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Emily L. Savage
1Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Yannick Schwab
9Cell Biology and Biophysics Unit / Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Rainer W. Friedrich
5Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, 4058, Switzerland
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Anna Kreshuk
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Christian Tischer
10Centre for Bioimage Analysis, Core Facilities, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Detlev Arendt
1Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany
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Summary

Animal bodies are composed of hundreds of cell types that differ in location, morphology, cytoarchitecture, and physiology. This is reflected by cell type-specific transcription factors and downstream effector genes implementing functional specialisation. Here, we establish and explore the link between cell type-specific gene expression and subcellular morphology for the entire body of the marine annelid Platynereis dumerilii. For this, we registered a whole-body cellular expression atlas to a high-resolution electron microscopy dataset, automatically segmented all cell somata and nuclei, and clustered the cells according to gene expression or morphological parameters. We show that collective gene expression most efficiently identifies spatially coherent groups of cells that match anatomical boundaries, which indicates that combinations of regionally expressed transcription factors specify tissue identity. We provide an integrated browser as a Fiji plugin to readily explore, analyse and visualise multimodal datasets with remote on-demand access to all available datasets.

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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-NC-ND 4.0 International license.
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Posted February 27, 2020.
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Whole-body integration of gene expression and single-cell morphology
Hernando M. Vergara, Constantin Pape, Kimberly I. Meechan, Valentyna Zinchenko, Christel Genoud, Adrian A. Wanner, Benjamin Titze, Rachel M. Templin, Paola Y. Bertucci, Oleg Simakov, Pedro Machado, Emily L. Savage, Yannick Schwab, Rainer W. Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt
bioRxiv 2020.02.26.961037; doi: https://doi.org/10.1101/2020.02.26.961037
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Whole-body integration of gene expression and single-cell morphology
Hernando M. Vergara, Constantin Pape, Kimberly I. Meechan, Valentyna Zinchenko, Christel Genoud, Adrian A. Wanner, Benjamin Titze, Rachel M. Templin, Paola Y. Bertucci, Oleg Simakov, Pedro Machado, Emily L. Savage, Yannick Schwab, Rainer W. Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt
bioRxiv 2020.02.26.961037; doi: https://doi.org/10.1101/2020.02.26.961037

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