Abstract
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.
Footnotes
The authors declare no competing financial interests.
This work is supported by a NeuroDevNet grant (P.P.); the University of British Columbia Bioinformatics Graduate Training Program (B.O.M.); a Canadian Institutes of Health Research postdoctoral fellowship (S.J.T.); the Campbell Family Mental Health Research Institute of Centre for Addiction and Mental Health (E.S. and B.R.); National Institutes of Health Grants MH077159 (to E.S.) and MH111099 and GM076990 (to P.P.); and an Natural Sciences and Engineering Research Council of Canada Discovery Grant (P.P.).
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
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