Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain
- Janelia Research Campus, Howard Hughes Medical Institute, United States
- Brandeis University, United States
Abstract
Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases we provide an extensive resource for further investigation of mouse neuronal cell types.
Data availability
Sequencing data have been deposited in NCBI GEO under accession number GSE79238.
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Transcriptional Basis of Neuronal Diversity in the Mammalian BrainNCBI Gene Expression Omnibus, GSE79238.
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Molecular architecture of the mouse nervous systemAvailable at http://mousebrain.org/downloads.html.
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A Single-Cell Atlas of Cell Types States, and Other Transcriptional Patterns from Nine Regions of the Adult Mouse BrainAvailable at http://dropviz.org/.
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Cell Diversity in the Mouse CortexAvailable at http://celltypes.brain-map.org/rnaseq.
Article and author information
Author details
Jayaram Chandrashekar
Funding
Howard Hughes Medical Institute
- Ken Sugino
- Anton Schulmann
- Lihua Wang
- David L Hunt
- Bryan M Hooks
- Dimitri Traenkner
- Jayaram Chandrashekar
- Andrew L Lemire
- Nelson Spruston
- Adam W Hantman
- Sacha B Nelson
National Eye Institute (EY022360)
- Erin Clark
- Yasuyuki Shima
- Sacha B Nelson
National Institute of Mental Health (MH105949)
- Erin Clark
- Yasuyuki Shima
- Sacha B Nelson
National Institute of Neurological Disorders and Stroke (NS075007)
- Erin Clark
- Yasuyuki Shima
- Sacha B Nelson
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Chris P Ponting, University of Edinburgh, United Kingdom
Ethics
Animal experimentation: All experiments were conducted in accordance with the requirements of theInstitutional Animal Care and Use Committees at Janelia Research Campus (protocol# not available) and Brandeis University (protocol#17001).
Version history
- Received: July 20, 2018
- Accepted: April 11, 2019
- Accepted Manuscript published: April 12, 2019 (version 1)
- Version of Record published: May 3, 2019 (version 2)
Copyright
© 2019, Sugino et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain
eLife 8:e38619.
https://doi.org/10.7554/eLife.38619
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