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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
Gene expression levels in 164 primary astrocytes and 83 neurosphere cells. Gene expression is shown as the number of cDNAs per cell. GS expression is shown in both linear and log10 scales; other genes are shown in log10 scale. Inset shows a more detailed histogram of Vim expression in astrocytes.
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Figure 2: Gene expression levels in 164 primary astrocytes and 83 neurosphere cells. Gene expression is shown as the number of cDNAs per cell. GS expression is shown in both linear and log10 scales; other genes are shown in log10 scale. Inset shows a more detailed histogram of Vim expression in astrocytes.

Mentions: The distributions of GS, GFAP, GFAPδ, Vim, Nes, ETBR, Sox2 and Nptx1 transcripts are shown in Figure 2 (see Supplementary Figure S2 for the second data set). Except for Vim, the distributions showed lognormal features, as described in other studies of mammalian cells (3,15,44). Lif, Syn and Wnt3 transcripts were detected in only few cells (Table 1 and Supplementary Table S2) and thus their distributions could not be reliably determined. The geometric and arithmetic means of the expression of individual genes are shown in Table 1. In a lognormal population, the geometric mean reflects the characteristic expression in a typical/median cell. The geometric mean is more conservative than the arithmetic mean. The latter overestimates the characteristic expression when expression levels are lognormally distributed.Figure 2.


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)

Gene expression levels in 164 primary astrocytes and 83 neurosphere cells. Gene expression is shown as the number of cDNAs per cell. GS expression is shown in both linear and log10 scales; other genes are shown in log10 scale. Inset shows a more detailed histogram of Vim expression in astrocytes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Gene expression levels in 164 primary astrocytes and 83 neurosphere cells. Gene expression is shown as the number of cDNAs per cell. GS expression is shown in both linear and log10 scales; other genes are shown in log10 scale. Inset shows a more detailed histogram of Vim expression in astrocytes.
Mentions: The distributions of GS, GFAP, GFAPδ, Vim, Nes, ETBR, Sox2 and Nptx1 transcripts are shown in Figure 2 (see Supplementary Figure S2 for the second data set). Except for Vim, the distributions showed lognormal features, as described in other studies of mammalian cells (3,15,44). Lif, Syn and Wnt3 transcripts were detected in only few cells (Table 1 and Supplementary Table S2) and thus their distributions could not be reliably determined. The geometric and arithmetic means of the expression of individual genes are shown in Table 1. In a lognormal population, the geometric mean reflects the characteristic expression in a typical/median cell. The geometric mean is more conservative than the arithmetic mean. The latter overestimates the characteristic expression when expression levels are lognormally distributed.Figure 2.

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