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Cell type prioritization in single-cell data
View ORCID ProfileMichael A. Skinnider, View ORCID ProfileJordan W. Squair, View ORCID ProfileClaudia Kathe, Mark A. Anderson, Matthieu Gautier, Kaya J.E. Matson, Marco Milano, Thomas H. Hutson, Quentin Barraud, Aaron A. Phillips, View ORCID ProfileLeonard J. Foster, View ORCID ProfileGioele La Manno, View ORCID ProfileAriel J. Levine, View ORCID ProfileGrégoire Courtine
doi: https://doi.org/10.1101/2019.12.20.884916
Michael A. Skinnider
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
2Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
Jordan W. Squair
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
3NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
4Departments of Physiology and Pharmacology, Clinical Neurosciences, Cardiac Sciences, Hotchkiss Brain Institute, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Alberta, Canada
5International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, British Columbia, Canada
Claudia Kathe
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Mark A. Anderson
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Matthieu Gautier
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Kaya J.E. Matson
6Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
Marco Milano
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Thomas H. Hutson
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Quentin Barraud
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Aaron A. Phillips
4Departments of Physiology and Pharmacology, Clinical Neurosciences, Cardiac Sciences, Hotchkiss Brain Institute, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Alberta, Canada
Leonard J. Foster
2Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
7Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
Gioele La Manno
8Center for Neuroprosthetics, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Ariel J. Levine
6Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
Grégoire Courtine
1Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
3NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
Abstract
We present a machine-learning method to prioritize the cell types most responsive to biological perturbations within high-dimensional single-cell data. We validate our method, Augur (https://github.com/neurorestore/Augur), on a compendium of single-cell RNA-seq, chromatin accessibility, and imaging transcriptomics datasets. We apply Augur to expose the neural circuits that enable walking after paralysis in response to spinal cord neurostimulation.
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.
Posted December 23, 2019.
Cell type prioritization in single-cell data
Michael A. Skinnider, Jordan W. Squair, Claudia Kathe, Mark A. Anderson, Matthieu Gautier, Kaya J.E. Matson, Marco Milano, Thomas H. Hutson, Quentin Barraud, Aaron A. Phillips, Leonard J. Foster, Gioele La Manno, Ariel J. Levine, Grégoire Courtine
bioRxiv 2019.12.20.884916; doi: https://doi.org/10.1101/2019.12.20.884916
Cell type prioritization in single-cell data
Michael A. Skinnider, Jordan W. Squair, Claudia Kathe, Mark A. Anderson, Matthieu Gautier, Kaya J.E. Matson, Marco Milano, Thomas H. Hutson, Quentin Barraud, Aaron A. Phillips, Leonard J. Foster, Gioele La Manno, Ariel J. Levine, Grégoire Courtine
bioRxiv 2019.12.20.884916; doi: https://doi.org/10.1101/2019.12.20.884916
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