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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; 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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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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This article has a correction. Please see:

  • Correction: Zhang et al., An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex - January 14, 2015

Abstract

The major cell classes of the brain differ in their developmental processes, metabolism, signaling, and function. To better understand the functions and interactions of the cell types that comprise these classes, we acutely purified representative populations of neurons, astrocytes, oligodendrocyte precursor cells, newly formed oligodendrocytes, myelinating oligodendrocytes, microglia, endothelial cells, and pericytes from mouse cerebral cortex. We generated a transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type. Bioinformatic analyses identified thousands of new cell type-enriched genes and splicing isoforms that will provide novel markers for cell identification, tools for genetic manipulation, and insights into the biology of the brain. For example, our data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the gene encoding the glycolytic enzyme pyruvate kinase. This dataset will provide a powerful new resource for understanding the development and function of the brain. To ensure the widespread distribution of these datasets, we have created a user-friendly website (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html) that provides a platform for analyzing and comparing transciption and alternative splicing profiles for various cell classes in the brain.

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