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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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Article Information

DOI 
https://doi.org/10.1523/ENEURO.0212-17.2017
PubMed 
29204516
Published By 
Society for Neuroscience
History 
  • Received June 13, 2017
  • Revision received October 25, 2017
  • Accepted October 31, 2017
  • Published online November 20, 2017.
Copyright & Usage 
Copyright © 2017 Mancarci et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.

Author Information

  1. B. Ogan Mancarci1,2,3,
  2. Lilah Toker2,3,
  3. Shreejoy J. Tripathy2,3,
  4. Brenna Li2,3,
  5. Brad Rocco4,5,
  6. Etienne Sibille4,5 and
  7. Paul Pavlidis2,3
  1. 1Graduate Program in Bioinformatics, University of British Columbia, Vancouver V6T 1Z4, Canada
  2. 2Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
  3. 3Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
  4. 4Campbell Family Mental Health Research Institute of CAMH
  5. 5Department of Psychiatry and the Department of Pharmacology and Toxicology, University of Toronto, Vancouver M5S 1A8, Canada
  1. Correspondence should be addressed to Paul Pavlidis, 177 Michael Smith Laboratories 2185 East Mall, University of British Columbia, Vancouver, BC V6T1Z4, Canada. E-mail: paul{at}msl.ubc.ca.
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Author contributions

  1. Author contributions: B.O.M., L.T., S.J.T., E.S., and P.P. designed research; B.O.M., L.T., B.L., and B.R. performed research; B.O.M. contributed unpublished reagents/analytic tools; B.O.M., L.T., S.J.T., and B.L. analyzed data; B.O.M., L.T., and P.P. wrote the paper.

Disclosures

  • The authors declare no competing financial interests.

  • This work is supported by a NeuroDevNet grant (P.P.); the University of British Columbia Bioinformatics Graduate Training Program (B.O.M.); a Canadian Institutes of Health Research postdoctoral fellowship (S.J.T.); the Campbell Family Mental Health Research Institute of Centre for Addiction and Mental Health (E.S. and B.R.); National Institutes of Health Grants MH077159 (to E.S.) and MH111099 and GM076990 (to P.P.); and an Natural Sciences and Engineering Research Council of Canada Discovery Grant (P.P.).

Funding

  • NeuroDevNet

  • UBC Bioinformatics Graduate Training Program

  • CIHR Post-doctoral fellowship

  • Campbell Family Mental Health Research Institute of CAMH

  • National Institutes of Health

    MH077159; MH111099; GM076990
  • NSERC Discovery Grant

Other Version

  • You are viewing the most recent version of this article.
  • previous version (November 20, 2017).

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AbstractFullPdf
Nov 20178000175
Dec 2017740687140
Total 20171540687315
Jan 201813415571
Feb 20187320460
Mar 20185112334
Apr 20184217859
May 20183713035
Jun 20184017487
Jul 20185212053
Aug 20184418588
Sep 20181918531
Oct 20183925237
Nov 20183536836
Dec 20181828427
Total 20185842358618
Jan 20192032523
Feb 20191936944
Mar 2019633616
Apr 20191231046
May 20191323629
Jun 20191017719
Jul 2019428833
Aug 20191133624
Oct 20191344124
Nov 20191133026
Dec 20191617419
Total 20191353322303
Jan 2020816013
Feb 2020716339
Mar 2020819613
May 20201119140
Jun 20201117830
Jul 2020918437
Aug 2020815828
Sep 20201421650
Oct 20201224440
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Dec 20201419629
Total 20201082054352
Jan 2021420435
Feb 2021417228
Mar 2021918335
Apr 2021518344
May 2021718146
Jun 2021919433
Jul 2021913340
Aug 2021622939
Sep 2021310017
Oct 2021812447
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Dec 2021210740
Total 2021741912446
Jan 2022615649
Feb 202286622
Mar 202288728
Apr 2022510526
May 202217634
Jun 202229428
Jul 202247221
Aug 202286126
Sep 202247429
Oct 202239522
Nov 202257430
Dec 2022109117
Total 2022641051332
Jan 202328829
Feb 202365911
Mar 20230649
Total 2023821149
Total2513115952415
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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
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Keywords

  • Cell Type
  • gene expression
  • Marker Gene
  • Microarray
  • RNA sequencing

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