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Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data Mancarci, B. Ogan; Toker, Lilah; Tripathy, Shreejoy J; Li, Brenna; Rocco, Brad; Sibille, Etienne; Pavlidis, Paul

Description

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 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 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 Neuroexpresso.org.

Item Metadata

Title	Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data
Creator	Mancarci, B. Ogan; Toker, Lilah; Tripathy, Shreejoy J; Li, Brenna; Rocco, Brad; Sibille, Etienne; Pavlidis, Paul
Contributor	Cuthill, Melissa
Date Issued	2019-03-05
Description	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 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 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 Neuroexpresso.org.
Subject	Medicine, Health and Life Sciences
Type	Dataset
Notes	http://hdl.handle.net/11272/10527
Date Available	2019-03-05
Provider	University of British Columbia Library
License	CC-BY 4.0
DOI	10.14288/1.0360718
URI	https://doi.org/10.5683/SP2/QZVIOI
Publisher DOI	https://doi.org/10.5683/SP2/QZVIOI
Rights URI	http://creativecommons.org/licenses/by/4.0
Aggregated Source Repository	Dataverse

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CC-BY 4.0