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A single-cell resolution gene expression atlas of the larval zebrafish brain

View ORCID ProfileInbal Shainer, Enrico Kuehn, Eva Laurell, Mariam Al Kassar, Nouwar Mokayes, Shachar Sherman, View ORCID ProfileJohannes Larsch, Michael Kunst, Herwig Baier
doi: https://doi.org/10.1101/2022.02.11.479024
Inbal Shainer
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
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  • ORCID record for Inbal Shainer
Enrico Kuehn
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
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Eva Laurell
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
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Mariam Al Kassar
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
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Nouwar Mokayes
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
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Shachar Sherman
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
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Johannes Larsch
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
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Michael Kunst
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
2Allen Institute for Brain Science, Seattle, WA 98109, USA
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Herwig Baier
1Max Planck Institute of Neurobiology, Martinsried. Current address: Max Planck Institute for Biological Intelligence, in foundation, Martinsried, Germany
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  • For correspondence: hbaier@neuro.mpg.de
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Abstract

The advent of multimodal brain atlases promises to accelerate discoveries in neuroscience by offering in silico queries of cell types, connectivity and gene expression in regions of interest. We employed multiplexed fluorescent in situ RNA hybridization chain reaction (HCR) to generate expression maps for an initial set of 200 marker genes across the larval zebrafish brain. The data were registered to the Max Planck Zebrafish Brain (mapzebrain) atlas, thus allowing co-visualization of gene expression patterns, single-neuron tracings, transgenic lines and anatomical segmentations. Additionally, brain activity maps of freely swimming larvae were generated at single-cell resolution using HCR labeling of the immediate-early gene cfos and integrated into the atlas. As a proof of concept, we identified a novel class of cerebellar eurydendroid cells that express calb2a, project to the hypothalamus and are activated in animals that have recently ingested food. Thus, a cellular-resolution gene expression atlas will not only help with rapid identification of marker genes for neuronal populations of interest, but also bridge the molecular and circuit levels by anchoring genetic information to functional activity maps and synaptic connectivity.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* Co-first author

  • http://fishatlas.neuro.mpg.de/

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 11, 2022.
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A single-cell resolution gene expression atlas of the larval zebrafish brain
Inbal Shainer, Enrico Kuehn, Eva Laurell, Mariam Al Kassar, Nouwar Mokayes, Shachar Sherman, Johannes Larsch, Michael Kunst, Herwig Baier
bioRxiv 2022.02.11.479024; doi: https://doi.org/10.1101/2022.02.11.479024
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A single-cell resolution gene expression atlas of the larval zebrafish brain
Inbal Shainer, Enrico Kuehn, Eva Laurell, Mariam Al Kassar, Nouwar Mokayes, Shachar Sherman, Johannes Larsch, Michael Kunst, Herwig Baier
bioRxiv 2022.02.11.479024; doi: https://doi.org/10.1101/2022.02.11.479024

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