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3D-Cardiomics: A spatial transcriptional atlas of the mammalian heart

Monika Mohenska, Nathalia M. Tan, Alex Tokolyi, Milena B. Furtado, Mauro W. Costa, Andrew J. Perry, Jessica Hatwell-Humble, Karel van Duijvenboden, Hieu T. Nim, Susan K. Nilsson, David R. Powell, Nadia A. Rosenthal, Fernando J. Rossello, Mirana Ramialison, View ORCID ProfileJose M. Polo
doi: https://doi.org/10.1101/792002
Monika Mohenska
1Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia
2Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
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Nathalia M. Tan
1Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia
2Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
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Alex Tokolyi
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
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Milena B. Furtado
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
4The Jackson Laboratory, Bar Harbor, ME, USA
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Mauro W. Costa
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
4The Jackson Laboratory, Bar Harbor, ME, USA
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Andrew J. Perry
5Monash Bioinformatics Platform, Monash University, Wellington Road, Clayton, Victoria, Australia
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Jessica Hatwell-Humble
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
6Biomedical Manufacturing, CSIRO Manufacturing, Bag 10, Clayton South, Australia
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Karel van Duijvenboden
7Department of Medical Biology, Academic Medical Centre, Amsterdam, The Netherlands
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Hieu T. Nim
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
8Faculty of Information Technology, Monash University, Clayton, Victoria, Australia
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Susan K. Nilsson
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
6Biomedical Manufacturing, CSIRO Manufacturing, Bag 10, Clayton South, Australia
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David R. Powell
5Monash Bioinformatics Platform, Monash University, Wellington Road, Clayton, Victoria, Australia
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Nadia A. Rosenthal
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
4The Jackson Laboratory, Bar Harbor, ME, USA
9National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Fernando J. Rossello
1Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia
2Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
11University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
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  • For correspondence: mirana.ramialison@monash.edu jose.polo@monash.edu frossello@unimelb.edu
Mirana Ramialison
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
10Systems Biology Institute Australia, Clayton, Victoria, Australia
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  • For correspondence: mirana.ramialison@monash.edu jose.polo@monash.edu frossello@unimelb.edu
Jose M. Polo
1Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia
2Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia
3Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
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  • ORCID record for Jose M. Polo
  • For correspondence: mirana.ramialison@monash.edu jose.polo@monash.edu frossello@unimelb.edu
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Abstract

Understanding spatial gene expression and regulation is key to uncovering developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information, but very few utilise intuitive true-to-life three-dimensional representations to analyze and visualize results. Here we combined spatial transcriptomics with 3D modelling to represent and interrogate, transcriptome-wide, three-dimensional gene expression and location in the mouse adult heart. Our study has unveiled specific subsets of genes that display complex spatial expression in organ sub-compartments. Also, we created a web-based user interface for spatial transcriptome analysis and visualization. The application may be accessed from http://3d-cardiomics.erc.monash.edu/.

Footnotes

  • ↵12 Equal Contribution

  • ↵13 Equal senior author

  • http://3d-cardiomics.erc.monash.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-ND 4.0 International license.
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Posted October 03, 2019.
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3D-Cardiomics: A spatial transcriptional atlas of the mammalian heart
Monika Mohenska, Nathalia M. Tan, Alex Tokolyi, Milena B. Furtado, Mauro W. Costa, Andrew J. Perry, Jessica Hatwell-Humble, Karel van Duijvenboden, Hieu T. Nim, Susan K. Nilsson, David R. Powell, Nadia A. Rosenthal, Fernando J. Rossello, Mirana Ramialison, Jose M. Polo
bioRxiv 792002; doi: https://doi.org/10.1101/792002
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3D-Cardiomics: A spatial transcriptional atlas of the mammalian heart
Monika Mohenska, Nathalia M. Tan, Alex Tokolyi, Milena B. Furtado, Mauro W. Costa, Andrew J. Perry, Jessica Hatwell-Humble, Karel van Duijvenboden, Hieu T. Nim, Susan K. Nilsson, David R. Powell, Nadia A. Rosenthal, Fernando J. Rossello, Mirana Ramialison, Jose M. Polo
bioRxiv 792002; doi: https://doi.org/10.1101/792002

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