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Research ArticleMethods/New Tools, Novel Tools and Methods

Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data

B. Ogan Mancarci, Lilah Toker, Shreejoy J. Tripathy, Brenna Li, Brad Rocco, Etienne Sibille and Paul Pavlidis
eNeuro 20 November 2017, 4 (6) ENEURO.0212-17.2017; DOI: https://doi.org/10.1523/ENEURO.0212-17.2017
B. Ogan Mancarci
1Graduate Program in Bioinformatics, University of British Columbia, Vancouver V6T 1Z4, Canada
2Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
3Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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Lilah Toker
2Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
3Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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Shreejoy J. Tripathy
2Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
3Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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Brenna Li
2Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
3Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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Brad Rocco
4Campbell Family Mental Health Research Institute of CAMH
5Department of Psychiatry and the Department of Pharmacology and Toxicology, University of Toronto, Vancouver M5S 1A8, Canada
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Etienne Sibille
4Campbell Family Mental Health Research Institute of CAMH
5Department of Psychiatry and the Department of Pharmacology and Toxicology, University of Toronto, Vancouver M5S 1A8, Canada
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Paul Pavlidis
2Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
3Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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eneuro: 4 (6)
eNeuro
Vol. 4, Issue 6
November/December 2017
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Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data
B. Ogan Mancarci, Lilah Toker, Shreejoy J. Tripathy, Brenna Li, Brad Rocco, Etienne Sibille, Paul Pavlidis
eNeuro 20 November 2017, 4 (6) ENEURO.0212-17.2017; DOI: 10.1523/ENEURO.0212-17.2017

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Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data
B. Ogan Mancarci, Lilah Toker, Shreejoy J. Tripathy, Brenna Li, Brad Rocco, Etienne Sibille, Paul Pavlidis
eNeuro 20 November 2017, 4 (6) ENEURO.0212-17.2017; DOI: 10.1523/ENEURO.0212-17.2017
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  • Article
    • Visual Abstract
    • Abstract
    • Significance Statement
    • Introduction
    • Materials and Methods
    • Allen Brain Atlas (ABA) ISH data
    • Validation of marker genes using external single-cell data
    • Preprocessing of microarray data
    • Estimation of MGPs
    • Code accessibility
    • Results
    • Discussion
    • Acknowledgments
    • Footnotes
    • References
    • Synthesis
    • Author Response
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Keywords

  • cell type
  • gene expression
  • Marker Gene
  • Microarray
  • RNA sequencing

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Methods/New Tools

  • Bicistronic expression of a high-performance calcium indicator and opsin for all-optical stimulation and imaging at cellular resolution
  • A Toolbox of Criteria for Distinguishing Cajal–Retzius Cells from Other Neuronal Types in the Postnatal Mouse Hippocampus
  • Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain
Show more Methods/New Tools

Novel Tools and Methods

  • Bicistronic expression of a high-performance calcium indicator and opsin for all-optical stimulation and imaging at cellular resolution
  • A Toolbox of Criteria for Distinguishing Cajal–Retzius Cells from Other Neuronal Types in the Postnatal Mouse Hippocampus
  • Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain
Show more Novel Tools and Methods

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  • Novel Tools and Methods

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