Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://web.stanford.edu/group/barres_lab/brain_rnaseq
Full name:
Description: 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.
Year founded: 2014
Last update:
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Country/Region: United States
Data type:
RNA
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Contact information

University/Institution: The University of Texas
Address: 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
City:
Province/State:
Country/Region: United States
Contact name (PI/Team): Wu JQ
Contact email (PI/Helpdesk): jiaqian.wu@uth.tmc.edu

Publications

25186741
An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. [PMID: 25186741]
Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O'Keeffe S, Phatnani HP, Guarnieri P, Caneda C, Ruderisch N, Deng S, Liddelow SA, Zhang C, Daneman R, Maniatis T, Barres BA, Wu JQ.

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.

J Neurosci. 2014:34(36) | 1423 Citations (from Europe PMC, 2021-01-23)

Ranking

All databases:
40/4740 (99.177%)
Expression:
7/871 (99.311%)
40
Total Rank
1,423
Citations
203.286
z-index

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Record metadata

Created on: 2018-01-28
Curated by:
Lina Ma [2019-07-29]
Lina Ma [2018-04-24]
Syed Sardar [2018-04-04]
Qi Wang [2018-01-27]