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Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles.

Huang Y, Ng FS, Jackson FR - G3 (Bethesda) (2015)

Bottom Line: These include genes important for metabolism and energy production, translation, chromatin modification, protein glycosylation, neuropeptide signaling, immune responses, vesicle-mediated trafficking or secretion, and the regulation of behavior.Among these functional classes, the expression of genes important for chromatin modification and vesicle-mediated trafficking or secretion is overrepresented in adult astrocytes based on Gene Ontology analysis.Certain genes with selective adult enrichment may mediate functions specific to this stage or may be important for the differentiation or maintenance of adult astrocytes, with the latter perhaps contributing to population heterogeneity.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts 02111.

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Fold enrichment by TRAP for 10 genes, relative to expression in total RNA. Enrichment was assayed by RNA-seq or QPCR.
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fig3: Fold enrichment by TRAP for 10 genes, relative to expression in total RNA. Enrichment was assayed by RNA-seq or QPCR.

Mentions: We compared the sequencing results from TRAP and total RNA samples to identify those with astrocyte-enriched expression. Two alternative methods (see Materials and Methods) revealed a similar number of genes with astrocyte-enriched expression with comparison of TRAP with the total RNA samples: Cuffdiff identified 3750, whereas DESeq identified 3795 genes. Of these, 3186 genes were found to have enriched expression by both programs (Table S1). Note that the values for total RNA and TRAP experiments in Table S1 and all other Supporting Information Tables represent mean values for three independent samples. We examined 10 genes with high, moderate, or low astrocyte-enriched expression—as judged by RNA-seq—using quantitative RT-PCR (QPCR). With the exception of one gene, enrichment values derived from the RNA-seq analysis were similar to those found by QPCR, verifying the sequencing results (Figure 3).


Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles.

Huang Y, Ng FS, Jackson FR - G3 (Bethesda) (2015)

Fold enrichment by TRAP for 10 genes, relative to expression in total RNA. Enrichment was assayed by RNA-seq or QPCR.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390571&req=5

fig3: Fold enrichment by TRAP for 10 genes, relative to expression in total RNA. Enrichment was assayed by RNA-seq or QPCR.
Mentions: We compared the sequencing results from TRAP and total RNA samples to identify those with astrocyte-enriched expression. Two alternative methods (see Materials and Methods) revealed a similar number of genes with astrocyte-enriched expression with comparison of TRAP with the total RNA samples: Cuffdiff identified 3750, whereas DESeq identified 3795 genes. Of these, 3186 genes were found to have enriched expression by both programs (Table S1). Note that the values for total RNA and TRAP experiments in Table S1 and all other Supporting Information Tables represent mean values for three independent samples. We examined 10 genes with high, moderate, or low astrocyte-enriched expression—as judged by RNA-seq—using quantitative RT-PCR (QPCR). With the exception of one gene, enrichment values derived from the RNA-seq analysis were similar to those found by QPCR, verifying the sequencing results (Figure 3).

Bottom Line: These include genes important for metabolism and energy production, translation, chromatin modification, protein glycosylation, neuropeptide signaling, immune responses, vesicle-mediated trafficking or secretion, and the regulation of behavior.Among these functional classes, the expression of genes important for chromatin modification and vesicle-mediated trafficking or secretion is overrepresented in adult astrocytes based on Gene Ontology analysis.Certain genes with selective adult enrichment may mediate functions specific to this stage or may be important for the differentiation or maintenance of adult astrocytes, with the latter perhaps contributing to population heterogeneity.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts 02111.

Show MeSH
Related in: MedlinePlus