Skip to main content

Main menu

  • HOME
  • CONTENT
    • Early Release
    • Featured
    • Current Issue
    • Issue Archive
    • Collections
    • Podcast
  • ALERTS
  • FOR AUTHORS
    • Information for Authors
    • Fees
    • Journal Clubs
    • eLetters
    • Submit
  • EDITORIAL BOARD
  • ABOUT
    • Overview
    • Advertise
    • For the Media
    • Rights and Permissions
    • Privacy Policy
    • Feedback
  • SUBSCRIBE

User menu

  • Log in
  • My Cart

Search

  • Advanced search
Journal of Neuroscience
  • Log in
  • My Cart
Journal of Neuroscience

Advanced Search

Submit a Manuscript
  • HOME
  • CONTENT
    • Early Release
    • Featured
    • Current Issue
    • Issue Archive
    • Collections
    • Podcast
  • ALERTS
  • FOR AUTHORS
    • Information for Authors
    • Fees
    • Journal Clubs
    • eLetters
    • Submit
  • EDITORIAL BOARD
  • ABOUT
    • Overview
    • Advertise
    • For the Media
    • Rights and Permissions
    • Privacy Policy
    • Feedback
  • SUBSCRIBE
PreviousNext
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,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
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,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Steven A. Sloan
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mariko L. Bennett
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anja R. Scholze
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sean O'Keeffe
4Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hemali P. Phatnani
4Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paolo Guarnieri
7Department of Systems Biology,
9Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Paolo Guarnieri
Christine Caneda
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nadine Ruderisch
5Department of Anatomy, University of California, San Francisco, San Francisco, California 94143-0452,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
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,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
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
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
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
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard Daneman
5Department of Anatomy, University of California, San Francisco, San Francisco, California 94143-0452,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tom Maniatis
4Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ben A. Barres
1Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ben A. Barres
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,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jia Qian Wu
  • Article
  • Figures & Data
  • Info & Metrics
  • eLetters
  • PDF
Loading

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
View Full Text
Back to top

In this issue

The Journal of Neuroscience: 34 (36)
Journal of Neuroscience
Vol. 34, Issue 36
3 Sep 2014
  • Table of Contents
  • Table of Contents (PDF)
  • About the Cover
  • Index by author
  • Advertising (PDF)
  • Ed Board (PDF)
Email

Thank you for sharing this Journal of Neuroscience article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
(Your Name) has forwarded a page to you from Journal of Neuroscience
(Your Name) thought you would be interested in this article in Journal of Neuroscience.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Print
View Full Page PDF
Citation Tools
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

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Respond to this article
Request Permissions
Share
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
del.icio.us logo Digg logo Reddit logo Twitter logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Jump to section

  • Article
    • Abstract
    • Introduction
    • Materials and Methods
    • Results
    • Discussion
    • Notes
    • Footnotes
    • References
  • Figures & Data
  • Info & Metrics
  • eLetters
  • PDF

Keywords

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

Responses to this article

Respond to this article

Jump to comment:

No eLetters have been published for this article.

Related Articles

Cited By...

More in this TOC Section

Articles

  • Choice Behavior Guided by Learned, But Not Innate, Taste Aversion Recruits the Orbitofrontal Cortex
  • Maturation of Spontaneous Firing Properties after Hearing Onset in Rat Auditory Nerve Fibers: Spontaneous Rates, Refractoriness, and Interfiber Correlations
  • Insulin Treatment Prevents Neuroinflammation and Neuronal Injury with Restored Neurobehavioral Function in Models of HIV/AIDS Neurodegeneration
Show more Articles

Cellular/Molecular

  • Control of Synaptic Levels of Nicotinic Acetylcholine Receptor by the Sequestering Subunit Dα5 and Secreted Scaffold Protein Hig
  • Multiple Subthreshold GPCR Signals Combined by the G-Proteins Gαq and Gαs Activate the Caenorhabditis elegans Egg-Laying Muscles
  • The SphK1/S1P Axis Regulates Synaptic Vesicle Endocytosis via TRPC5 Channels
Show more Cellular/Molecular
  • Home
  • Alerts
  • Visit Society for Neuroscience on Facebook
  • Follow Society for Neuroscience on Twitter
  • Follow Society for Neuroscience on LinkedIn
  • Visit Society for Neuroscience on Youtube
  • Follow our RSS feeds

Content

  • Early Release
  • Current Issue
  • Issue Archive
  • Collections

Information

  • For Authors
  • For Advertisers
  • For the Media
  • For Subscribers

About

  • About the Journal
  • Editorial Board
  • Privacy Policy
  • Contact
(JNeurosci logo)
(SfN logo)

Copyright © 2023 by the Society for Neuroscience.
JNeurosci Online ISSN: 1529-2401

The ideas and opinions expressed in JNeurosci do not necessarily reflect those of SfN or the JNeurosci Editorial Board. Publication of an advertisement or other product mention in JNeurosci should not be construed as an endorsement of the manufacturer’s claims. SfN does not assume any responsibility for any injury and/or damage to persons or property arising from or related to any use of any material contained in JNeurosci.