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Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations.

Ståhlberg A, Andersson D, Aurelius J, Faiz M, Pekna M, Kubista M, Pekny M - Nucleic Acids Res. (2010)

Bottom Line: We show how subpopulations of cells can be identified at single-cell level using unsupervised algorithms and that gene correlations can be used to identify differences in activity of important transcriptional pathways.We identified two subpopulations of astrocytes with distinct gene expression profiles.One had an expression profile very similar to that of neurosphere cells, whereas the other showed characteristics of activated astrocytes in vivo.

View Article: PubMed Central - PubMed

Affiliation: Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 9A, 413 90 Gothenburg, Sweden. anders.stahlberg@neuro.gu.se

ABSTRACT
Single-cell gene expression levels show substantial variations among cells in seemingly homogenous populations. Astrocytes perform many control and regulatory functions in the central nervous system. In contrast to neurons, we have limited knowledge about functional diversity of astrocytes and its molecular basis. To study astrocyte heterogeneity and stem/progenitor cell properties of astrocytes, we used single-cell gene expression profiling in primary mouse astrocytes and dissociated mouse neurosphere cells. The transcript number variability for astrocytes showed lognormal features and revealed that cells in primary cultures to a large extent co-express markers of astrocytes and neural stem/progenitor cells. We show how subpopulations of cells can be identified at single-cell level using unsupervised algorithms and that gene correlations can be used to identify differences in activity of important transcriptional pathways. We identified two subpopulations of astrocytes with distinct gene expression profiles. One had an expression profile very similar to that of neurosphere cells, whereas the other showed characteristics of activated astrocytes in vivo.

Show MeSH
Classification of neurosphere cells. Principal component and potential curve analysis were used to classify neurosphere cells (black) based on the expression profiles of the two subpopulations of astrocytes. Each dot represents one cell: red dots are cells with low expression of Vim, GFAP, GFAPδ, Nes, ETBR and Sox2; green dots are cells with high expression of Vim, GFAP, GFAPδ, Nes, ETBR and Sox2.
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Figure 5: Classification of neurosphere cells. Principal component and potential curve analysis were used to classify neurosphere cells (black) based on the expression profiles of the two subpopulations of astrocytes. Each dot represents one cell: red dots are cells with low expression of Vim, GFAP, GFAPδ, Nes, ETBR and Sox2; green dots are cells with high expression of Vim, GFAP, GFAPδ, Nes, ETBR and Sox2.

Mentions: Finally, we determined if the neurosphere cells had gene expression profile similar to any of the astrocyte subpopulations using PCA and potential curve analysis (Figure 5). The principal component space was calculated using the expression profiles of the astrocytes only. When the neurosphere cells were positioned in this space based on their expression profiles, the classification revealed a high degree of similarity between gene expression profile of neurosphere cells and the astrocyte subpopulation characterized by low expression of Vim, GS, GFAP, GFAPδ, Nes, Sox2 and ETBR.Figure 5.


Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations.

Ståhlberg A, Andersson D, Aurelius J, Faiz M, Pekna M, Kubista M, Pekny M - Nucleic Acids Res. (2010)

Classification of neurosphere cells. Principal component and potential curve analysis were used to classify neurosphere cells (black) based on the expression profiles of the two subpopulations of astrocytes. Each dot represents one cell: red dots are cells with low expression of Vim, GFAP, GFAPδ, Nes, ETBR and Sox2; green dots are cells with high expression of Vim, GFAP, GFAPδ, Nes, ETBR and Sox2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3045576&req=5

Figure 5: Classification of neurosphere cells. Principal component and potential curve analysis were used to classify neurosphere cells (black) based on the expression profiles of the two subpopulations of astrocytes. Each dot represents one cell: red dots are cells with low expression of Vim, GFAP, GFAPδ, Nes, ETBR and Sox2; green dots are cells with high expression of Vim, GFAP, GFAPδ, Nes, ETBR and Sox2.
Mentions: Finally, we determined if the neurosphere cells had gene expression profile similar to any of the astrocyte subpopulations using PCA and potential curve analysis (Figure 5). The principal component space was calculated using the expression profiles of the astrocytes only. When the neurosphere cells were positioned in this space based on their expression profiles, the classification revealed a high degree of similarity between gene expression profile of neurosphere cells and the astrocyte subpopulation characterized by low expression of Vim, GS, GFAP, GFAPδ, Nes, Sox2 and ETBR.Figure 5.

Bottom Line: We show how subpopulations of cells can be identified at single-cell level using unsupervised algorithms and that gene correlations can be used to identify differences in activity of important transcriptional pathways.We identified two subpopulations of astrocytes with distinct gene expression profiles.One had an expression profile very similar to that of neurosphere cells, whereas the other showed characteristics of activated astrocytes in vivo.

View Article: PubMed Central - PubMed

Affiliation: Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 9A, 413 90 Gothenburg, Sweden. anders.stahlberg@neuro.gu.se

ABSTRACT
Single-cell gene expression levels show substantial variations among cells in seemingly homogenous populations. Astrocytes perform many control and regulatory functions in the central nervous system. In contrast to neurons, we have limited knowledge about functional diversity of astrocytes and its molecular basis. To study astrocyte heterogeneity and stem/progenitor cell properties of astrocytes, we used single-cell gene expression profiling in primary mouse astrocytes and dissociated mouse neurosphere cells. The transcript number variability for astrocytes showed lognormal features and revealed that cells in primary cultures to a large extent co-express markers of astrocytes and neural stem/progenitor cells. We show how subpopulations of cells can be identified at single-cell level using unsupervised algorithms and that gene correlations can be used to identify differences in activity of important transcriptional pathways. We identified two subpopulations of astrocytes with distinct gene expression profiles. One had an expression profile very similar to that of neurosphere cells, whereas the other showed characteristics of activated astrocytes in vivo.

Show MeSH