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Dlott, G., Maul, J. E., Buyer, J. & Yarwood, S. Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils.
In the case of individual comparisons of samples, gene ratios were calculated against the mean of all control samples.
We compared samples individually for significant genes i.e. gene ratios, among experimental setups, using a two-tailed z-test, which we refer to as "inter-experimental".
Fungal∶bacterial rRNA gene ratios and the abundance of fungal- and bacterial-feeding nematodes did not significantly differ among the three tree species.
Indeed, by using these gene ratios, a host target gene is directly compared to another host target gene within the same sample removing the potential bias induced by different symbiont densities.
Corresponding values for the gltA/MIF gene ratios for the Rickettsia sp. were 4.3 (1.5 7.0) for the PBS control, 1.8 (1.4–2.1) for rifampin treatment (p<0.01), and 1.4 (1.1 1.7) for tetracycline treatment (p<0.001).
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Wolbachia-gene to reference-gene ratios were obtained following the method in [37].
Furthermore, we find no significant differences in the CpG-to-gene ratios between HCNE poor ST miRNAs and bystander genes or other transcription factors.
In addition, the CpG-to-gene ratios of HCNE poor ST miRNAs is significantly lower when compared to GRB target genes/other CGI genes.
However, we did not find significant differences in the CpG-to-gene ratios between HCNE enriched ST miRNAs and HCNE poor ST miRNAs, which could be explained by the small sample size.
This indicates that the distribution of CpG-to-gene ratios of HCNE enriched ST miRNAs is more similar to GRB target genes than that of HCNE poor ST miRNAs.
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