Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Nov 30;4(6):ENEURO.0212-17.2017.
doi: 10.1523/ENEURO.0212-17.2017. eCollection 2017 Nov-Dec.

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

Affiliations

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

B Ogan Mancarci et al. eNeuro. .

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.

Keywords: RNA sequencing; cell type; gene expression; marker gene; microarray.

PubMed Disclaimer

Figures

None
Graphical abstract
Figure 1.
Figure 1.
Mouse brain cell type-specific expression database compiled from publicly available datasets. A, Workflow of the study. Cell type-specific expression profiles are collected from publicly available datasets and personal communications. Acquired samples are grouped based on cell type and brain region. Marker genes are selected per brain region for all cell types. Marker genes are biologically and computationally validated and used in estimation of cell type proportions. B, Brain region hierarchy used in the study. Samples included in a brain region based on the region they were extracted from. For instance, dopaminergic cells isolated from the midbrain were included when selecting marker genes in the context of brainstem and whole brain, and microglia extracted from whole brain isolates were added to all brain regions.
Figure 2.
Figure 2.
The NeuroExpresso.org web application. The application allows easy visualization of gene expression across cell types in brain regions. Depicted is the expression of cell types from neocortex region. Alternatively, cell types can be grouped based on their primary neurotransmitter or the purification type. The application can be reached at www.neuroexpresso.org.
Figure 3.
Figure 3.
Marker genes are selected for mouse brain cell types and used to estimate cell type profiles. A, Expression of top marker genes selected for cell cortical cell types in cell types represented by RNA-seq (left) and microarray (right) data in NeuroExpresso. Expression levels were normalized per gene to be between 0 and 1 for each dataset. B, Expression of Fam114a1 in neocortex in microarray (top) and RNA-seq (bottom) datasets. Fam114a1 is a proposed fast spiking basket cell marker. It was not selected as a marker in this study due to its high expression in oligodendrocytes and S100a10 expressing pyramidal cells that were both absent from the original study.
Figure 4.
Figure 4.
Validation of candidate markers using the ABA. A, ISH images from the ABA. Rightmost panels show the location of the image in the brain according to the Allen Brain mouse reference atlas. Panels on the left show the ISH image and normalized expression level of known and novel dentate gyrus granule cell (upper panels) and Purkinje cell (lower panels) markers. B, Validation status of marker genes detected for Purkinje and dentate gyrus granule cells. Figures used for validation and validation statuses of individual marker genes can be found in Extended Data (Extended Data Fig. 4-1,2,3,4).
Figure 5.
Figure 5.
Single-plane image of mouse sensorimotor cortex labeled for Pvalb, Slc32a1, and Cox6a2 mRNAs and counterstained with NeuroTrace. Arrows indicate Cox6a2+ neurons. Scale bar: 10 µm.
Figure 6.
Figure 6.
NeuroExpresso reveals novel gene expression patterns. A, Expression of cholinergic, GABAergic, and glutamatergic markers in cholinergic cells from forebrain and thalamus. Forebrain cholinergic neurons express GABAergic markers while thalamus (hubenular) cholinergic neurons express glutamatergic markers. B, left, Expression of Ddc in oligodendrocyte samples from Cahoy et al. (2008), Doyle et al. (2008), and Fomchenko et al. (2011) datasets and in comparison to dopaminergic cells and other (nonoligodendrocyte) cell types from the neocortex in the microarray dataset. In all three datasets, expression of Ddc in oligodendrocytes is comparable to expression in dopaminergic cells and is higher than in any of the other cortical cells. Oligodendrocyte samples show higher than background levels of expression across datasets. Right, Ddc expression in oligodendrocytes, OPCs, and other cell types from Tasic et al. (2016) single-cell dataset. C, Bimodal gene expression in two dopaminergic cell isolates by different labs. Genes shown are labeled as marker genes in the context of midbrain if the two cell isolates are labeled as different cell types.
Figure 7.
Figure 7.
MGPs reveal cell type-specific changes in whole tissue data. A, Estimation of cell type profiles for cortical cells in frontal cortex and white matter. Values are normalized to be between 0 and 1. (***p < 0.001). B, left, Oligodendrocyte MGPs in Stanley C cohort. Right, Morphology-based oligodendrocyte counts of Stanley C cohort. Figure adapted from Uranova et al. (2004). C, Estimations of dopaminergic cell MGPs in substantia nigra of controls and PD patients. Values are relative and are normalized to be between 0 and 1 and are not reflective of absolute proportions (**p < 0.01, ***p < 0.001).

Similar articles

Cited by

References

    1. Anandasabapathy N, Victora GD, Meredith M, Feder R, Dong B, Kluger C, Yao K, Dustin ML, Nussenzweig MC, Steinman RM, Liu K (2011) Flt3L controls the development of radiosensitive dendritic cells in the meninges and choroid plexus of the steady-state mouse brain. J Exp Med 208:1695–1705. 10.1084/jem.20102657 - DOI - PMC - PubMed
    1. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A (2013) NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res 41:D991–D995. - PMC - PubMed
    1. Beckervordersandforth R, Tripathi P, Ninkovic J, Bayam E, Lepier A, Stempfhuber B, Kirchhoff F, Hirrlinger J, Haslinger A, Lie DC, Beckers J, Yoder B, Irmler M, Götz M (2010) In vivo fate mapping and expression analysis reveals molecular hallmarks of prospectively isolated adult neural stem cells. Cell Stem Cell 7:744–758. 10.1016/j.stem.2010.11.017 - DOI - PubMed
    1. Bellesi M, Pfister-Genskow M, Maret S, Keles S, Tononi G, Cirelli C (2013) Effects of sleep and wake on oligodendrocytes and their precursors. J Neurosci 33:14288–14300. 10.1523/JNEUROSCI.5102-12.2013 - DOI - PMC - PubMed
    1. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57:289–300.

LinkOut - more resources