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Articles, Cellular/Molecular

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

Ye Zhang, Kenian Chen, Steven A. Sloan, Mariko L. Bennett, Anja R. Scholze, Sean O'Keeffe, Hemali P. Phatnani, Paolo Guarnieri, Christine Caneda, Nadine Ruderisch, Shuyun Deng, Shane A. Liddelow, Chaolin Zhang, Richard Daneman, Tom Maniatis, Ben A. Barres and Jia Qian Wu
Journal of Neuroscience 3 September 2014, 34 (36) 11929-11947; DOI: https://doi.org/10.1523/JNEUROSCI.1860-14.2014
Ye Zhang
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
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Kenian Chen
2The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, Texas 77057,
3Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, Texas 77057,
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Steven A. Sloan
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
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Mariko L. Bennett
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
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Anja R. Scholze
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
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Sean O'Keeffe
4Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032,
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Hemali P. Phatnani
4Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032,
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Paolo Guarnieri
7Department of Systems Biology,
9Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032
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  • ORCID record for Paolo Guarnieri
Christine Caneda
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
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Nadine Ruderisch
5Department of Anatomy, University of California, San Francisco, San Francisco, California 94143-0452,
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Shuyun Deng
2The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, Texas 77057,
3Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, Texas 77057,
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Shane A. Liddelow
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
6Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia 3010, and
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Chaolin Zhang
4Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032,
7Department of Systems Biology,
8Center for Motor Neuron Biology and Disease, and
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Richard Daneman
5Department of Anatomy, University of California, San Francisco, San Francisco, California 94143-0452,
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Tom Maniatis
4Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032,
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Ben A. Barres
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
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Jia Qian Wu
2The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, Texas 77057,
3Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, Texas 77057,
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Article Information

DOI 
https://doi.org/10.1523/JNEUROSCI.1860-14.2014
PubMed 
25186741
Published By 
Society for Neuroscience
History 
  • Received May 7, 2014
  • Revision received July 11, 2014
  • Accepted July 22, 2014
  • First published September 3, 2014.
  • Version of record published September 3, 2014.
Copyright & Usage 
Copyright © 2014 the authors 0270-6474/14/3411929-19$15.00/0

Author Information

  1. Ye Zhang1,*,
  2. Kenian Chen2,3,*,
  3. Steven A. Sloan1,*,
  4. Mariko L. Bennett1,
  5. Anja R. Scholze1,
  6. Sean O'Keeffe4,
  7. Hemali P. Phatnani4,
  8. Paolo Guarnieri7,9,
  9. Christine Caneda1,
  10. Nadine Ruderisch5,
  11. Shuyun Deng2,3,
  12. Shane A. Liddelow1,6,
  13. Chaolin Zhang4,7,8,
  14. Richard Daneman5,
  15. Tom Maniatis4,
  16. Ben A. Barres1,†, and
  17. Jia Qian Wu2,3,†
  1. 1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
  2. 2The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, Texas 77057,
  3. 3Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, Texas 77057,
  4. 4Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032,
  5. 5Department of Anatomy, University of California, San Francisco, San Francisco, California 94143-0452,
  6. 6Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia 3010, and
  7. 7Department of Systems Biology,
  8. 8Center for Motor Neuron Biology and Disease, and
  9. 9Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032
View Full Text

Author contributions

  1. Author contributions: Y.Z., S.A.S., M.L.B., R.D., T.M., B.A.B., and J.Q.W. designed research; Y.Z., S.A.S., M.L.B., A.R.S., C.C., N.R., and S.D. performed research; S.A.L. and C.Z. contributed unpublished reagents/analytic tools; Y.Z., K.C., S.A.S., M.L.B., S.O., H.P.P., and P.G. analyzed data; Y.Z., S.A.S., and B.A.B. wrote the paper.

  2. ↵*Y.Z., K.C., and S.A.S. contributed equally to this work.

  3. ↵†B.A.B. and J.Q.W. contributed equally to this work.

View Abstract

Disclosures

    • Received May 7, 2014.
    • Revision received July 11, 2014.
    • Accepted July 22, 2014.
  • This work is supported by National Institutes of Health Grants R01 MH09955501 and R01 NS08170301 (B.A.B.), T32GM007365 with additional support from Stanford School of Medicine and its Medical Scientist Training Program (S.S.), and R00 GM95713 (C.Z.), a Berry Postdoctoral Fellowship (Y.Z.), and a National Health and Medical Research Council of Australia C. J. Martin Fellowship (S.L.). J.Q.W., K.C., and S.D. are supported by National Institutes of Health and the Staman Ogilvie Fund–Memorial Hermann Foundation. We thank Dr. Dritan Agalliu for Cldn5 expression plasmid and Vincent and Stella Coates for their generous support.

  • The authors declare no competing financial interests.

  • Correspondence should be addressed to either of the following: Ye Zhang, Stanford University School of Medicine, Department of Neurobiology, 299 Campus Drive, Fairchild Building, Stanford, California 94305-5125, zhangye{at}stanford.edu; or Jia Qian Wu, University of Texas Medical School, 1825 Pressler Street, SRB-630.01, Houston, TX 77030. jiaqian.wu{at}uth.tmc.edu

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AbstractFullPdf
Sep 2014561711531229
Oct 20141309581437
Nov 2014840453327
Dec 2014650375321
Total 2014841625622314
Jan 2015830441285
Feb 2015678357251
Mar 2015671533362
Apr 2015600459312
May 2015661541344
Jun 2015606468316
Jul 2015581576322
Aug 2015465503290
Sep 2015565479308
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Dec 2015548598257
Total 2015728762013730
Jan 2016874630364
Feb 2016940696313
Mar 2016939624344
Apr 2016847541409
May 2016941649431
Jun 2016821573327
Jul 2016803624289
Aug 2016865570280
Sep 2016845484316
Oct 2016683596346
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Dec 2016418745344
Total 2016943974934152
Jan 2017462903381
Feb 2017441915372
Mar 2017491966432
Apr 2017406683334
May 2017491738392
Jun 2017381591294
Jul 2017349712263
Aug 2017394650356
Sep 2017405627326
Oct 2017410961323
Nov 2017421904339
Dec 2017327698271
Total 2017497893484083
Jan 2018465799346
Feb 2018509815329
Mar 2018549818338
Apr 2018509704312
May 2018494774315
Jun 2018411689300
Jul 2018392721303
Aug 2018390770310
Sep 2018342708282
Oct 2018420826296
Nov 2018350934307
Dec 20183541003239
Total 2018518595613677
Jan 20194071116303
Feb 2019344786277
Mar 2019339726287
Apr 2019333780274
May 20194371124341
Jun 20193101045316
Jul 2019337957347
Aug 2019328983346
Sep 20193551324288
Oct 20194181773318
Nov 2019346981276
Dec 2019303810275
Total 20194257124053648
Jan 20203131014259
Feb 2020316923366
Mar 20202421160394
Apr 20202371296484
May 20202551178520
Jun 20202151008355
Jul 2020179923333
Aug 2020156815301
Sep 2020229997357
Oct 20202321091395
Nov 2020208949331
Dec 2020206979351
Total 20202788123334446
Jan 20211961182350
Feb 20212471120356
Mar 20212361196445
Apr 20211871115367
May 20211731090347
Jun 20211811200317
Jul 20211541118291
Aug 20211501011287
Sep 20212131076359
Oct 20212191197446
Nov 20211931444460
Dec 20211441422373
Total 20212293141714398
Jan 20222031903417
Feb 20221832047367
Mar 20222251173418
Apr 20221941108453
May 20221961120492
Jun 2022144755311
Total 2022114581062458
Total457888218032906
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The Journal of Neuroscience: 34 (36)
Journal of Neuroscience
Vol. 34, Issue 36
3 Sep 2014
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An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
Ye Zhang, Kenian Chen, Steven A. Sloan, Mariko L. Bennett, Anja R. Scholze, Sean O'Keeffe, Hemali P. Phatnani, Paolo Guarnieri, Christine Caneda, Nadine Ruderisch, Shuyun Deng, Shane A. Liddelow, Chaolin Zhang, Richard Daneman, Tom Maniatis, Ben A. Barres, Jia Qian Wu
Journal of Neuroscience 3 September 2014, 34 (36) 11929-11947; DOI: 10.1523/JNEUROSCI.1860-14.2014

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An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
Ye Zhang, Kenian Chen, Steven A. Sloan, Mariko L. Bennett, Anja R. Scholze, Sean O'Keeffe, Hemali P. Phatnani, Paolo Guarnieri, Christine Caneda, Nadine Ruderisch, Shuyun Deng, Shane A. Liddelow, Chaolin Zhang, Richard Daneman, Tom Maniatis, Ben A. Barres, Jia Qian Wu
Journal of Neuroscience 3 September 2014, 34 (36) 11929-11947; DOI: 10.1523/JNEUROSCI.1860-14.2014
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Keywords

  • alternative splicing
  • astrocytes
  • microglia
  • oligodendrocytes
  • transcriptome
  • vascular cells

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