PMID- 25186741 OWN - NLM STAT- MEDLINE DCOM- 20141110 LR - 20220409 IS - 1529-2401 (Electronic) IS - 0270-6474 (Print) IS - 0270-6474 (Linking) VI - 34 IP - 36 DP - 2014 Sep 3 TI - An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. PG - 11929-47 LID - 10.1523/JNEUROSCI.1860-14.2014 [doi] AB - 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. CI - Copyright (c) 2014 the authors 0270-6474/14/3411929-19$15.00/0. FAU - Zhang, Ye AU - Zhang Y AD - Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125, zhangye@stanford.edu jiaqian.wu@uth.tmc.edu. FAU - Chen, Kenian AU - Chen K AD - The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, Texas 77057, Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, Texas 77057. FAU - Sloan, Steven A AU - Sloan SA AD - Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125. FAU - Bennett, Mariko L AU - Bennett ML AD - Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125. FAU - Scholze, Anja R AU - Scholze AR AD - Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125. FAU - O'Keeffe, Sean AU - O'Keeffe S AD - Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032. FAU - Phatnani, Hemali P AU - Phatnani HP AD - Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032. FAU - Guarnieri, Paolo AU - Guarnieri P AUID- ORCID: 0000-0002-6979-2638 AD - Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032. FAU - Caneda, Christine AU - Caneda C AD - Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125. FAU - Ruderisch, Nadine AU - Ruderisch N AD - Department of Anatomy, University of California, San Francisco, San Francisco, California 94143-0452. FAU - Deng, Shuyun AU - Deng S AD - The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, Texas 77057, Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, Texas 77057. FAU - Liddelow, Shane A AU - Liddelow SA AD - Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125, Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia 3010, and. FAU - Zhang, Chaolin AU - Zhang C AD - Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032, Department of Systems Biology, Center for Motor Neuron Biology and Disease, and. FAU - Daneman, Richard AU - Daneman R AD - Department of Anatomy, University of California, San Francisco, San Francisco, California 94143-0452. FAU - Maniatis, Tom AU - Maniatis T AD - Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032. FAU - Barres, Ben A AU - Barres BA AUID- ORCID: 0000-0003-2905-4136 AD - Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305-5125. FAU - Wu, Jian Qian AU - Wu JQ AUID- ORCID: 0000-0002-6938-6648 AD - The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, Texas 77057, Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, Texas 77057, zhangye@stanford.edu jiaqian.wu@uth.tmc.edu. LA - eng GR - R01 MH09955501/MH/NIMH NIH HHS/United States GR - R01 NS08170301/NS/NINDS NIH HHS/United States GR - R00 NS089780/NS/NINDS NIH HHS/United States GR - R00 GM095713/GM/NIGMS NIH HHS/United States GR - K99 NS089780/NS/NINDS NIH HHS/United States GR - T32GM007365/GM/NIGMS NIH HHS/United States GR - R01 NS081703/NS/NINDS NIH HHS/United States GR - T32 GM007365/GM/NIGMS NIH HHS/United States GR - R00 GM95713/GM/NIGMS NIH HHS/United States GR - R01 MH099555/MH/NIMH NIH HHS/United States GR - T32 GM007790/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - J Neurosci JT - The Journal of neuroscience : the official journal of the Society for Neuroscience JID - 8102140 SB - IM EIN - J Neurosci. 2015 Jan 14;35(2):846-6 MH - *Alternative Splicing MH - Animals MH - Cerebral Cortex/blood supply/cytology/*metabolism MH - *Databases, Nucleic Acid MH - Endothelium, Vascular/*metabolism MH - Mice MH - Neuroglia/*metabolism MH - Neurons/*metabolism MH - Sequence Analysis, RNA MH - *Transcriptome PMC - PMC4152602 OTO - NOTNLM OT - alternative splicing OT - astrocytes OT - microglia OT - oligodendrocytes OT - transcriptome OT - vascular cells EDAT- 2014/09/05 06:00 MHDA- 2014/11/11 06:00 PMCR- 2015/03/03 CRDT- 2014/09/05 06:00 PHST- 2014/09/05 06:00 [entrez] PHST- 2014/09/05 06:00 [pubmed] PHST- 2014/11/11 06:00 [medline] PHST- 2015/03/03 00:00 [pmc-release] AID - 34/36/11929 [pii] AID - 1860-14 [pii] AID - 10.1523/JNEUROSCI.1860-14.2014 [doi] PST - ppublish SO - J Neurosci. 2014 Sep 3;34(36):11929-47. doi: 10.1523/JNEUROSCI.1860-14.2014.