Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data

Establishing the molecular diversity of cell types is crucial for the study of the nervous system. We compiled a cross-laboratory database of mouse brain cell type-specific transcriptomes from 36 major cell types from across the mammalian brain using rigorously curated published data from pooled cel...

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Bibliographic Details
Published in:eNeuro 2017-11, Vol.4 (6), p.ENEURO.0212-17.2017
Main Authors: Mancarci, B Ogan, Toker, Lilah, Tripathy, Shreejoy J, Li, Brenna, Rocco, Brad, Sibille, Etienne, Pavlidis, Paul
Format: Article
Language:English
Subjects:
Animals
Brain
Databases, Genetic
Internet
Methods/New Tools
Mice
Transcriptome
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Summary:Establishing the molecular diversity of cell types is crucial for the study of the nervous system. We compiled a cross-laboratory database of mouse brain cell type-specific transcriptomes from 36 major cell types from across the mammalian brain using rigorously curated published data from pooled cell type microarray and single-cell RNA-sequencing (RNA-seq) studies. We used these data to identify cell type-specific marker genes, discovering a substantial number of novel markers, many of which we validated using computational and experimental approaches. We further demonstrate that summarized expression of marker gene sets (MGSs) in bulk tissue data can be used to estimate the relative cell type abundance across samples. To facilitate use of this expanding resource, we provide a user-friendly web interface at www.neuroexpresso.org.
ISSN:2373-2822
2373-2822
DOI:10.1523/ENEURO.0212-17.2017