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Figure 2 | BMC Genomics

Figure 2

From: Complementary transcriptomic, lipidomic, and targeted functional genetic analyses in cultured Drosophila cells highlight the role of glycerophospholipid metabolism in Flock House virus RNA replication

Figure 2

FHV infection and replicon expression upregulate partially overlapping sets of Drosophila genes. (A) Venn diagram indicating the number of upregulated genes unique to FHV-infected cells (white circle), unique to FHV replicon-expressing cells (grey circle), or upregulated with both (black convergence). Total numbers of genes are given within the indicated regions, and complete lists and descriptions of genes are provided in Table 1 and as Additional Files 1, 2 and 3. Specific upregulated genes involved in lipid metabolism, as identified by GO terms, are shown by either their gene symbols or CG designations. (B) Semi-quantitative RT-PCR validation of Cct1 and Cct2 mRNA upregulation in Drosophila S2 cells infected with FHV. Decreasing amounts of cDNA generated by RT with oligo-dT primers and equivalent amounts of total RNA from mock (upper gel) or FHV-infected S2 cells (lower gel) were amplified with gene-specific primers for Drosophila actin (Act5C), Cct1, or Cct2, and PCR products were examined by agarose gel electrophoresis and ethidium bromide staining. The expression level of the Act5C transcript in microarray experiments was not significantly altered with FHV infection or replicon expression. Densitometry analysis of PCR products generated from cDNA dilutions that produced submaximal signals showed that FHV infection induced 2.0 ± 0.2 and 2.3 ± 0.3 fold increases in Cct1 and Cct2 mRNA levels, respectively, consistent with quantitative microarray results (see Additional File 1). (C) Semi-quantitative RT-PCR validation of Cct1 and Cct2 mRNA upregulation in Drosophila S2 cells expressing an FHV replicon. RT-PCR was performed as described above with total RNA from S2 cells containing the control plasmid pS2F1fs (upper gel) or FHV replicon-encoding plasmid pS2F1 (lower gel). Densitometry analysis of PCR products as described above showed that FHV replicon expression induced 1.9 ± 0.2 and 2.8 ± 0.9 fold increases in Cct1 and Cct2 mRNA levels, respectively, consistent with quantitative microarray results (see Additional File 2).

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