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Fig. 2 | BioData Mining

Fig. 2

From: RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

Fig. 2

Experimental design and evaluation of moose 2. a Triplicate E. coli MG1655 cultures were treated with MMC, and total RNA samples were sequenced on an Illumina platform. b Variation plot for expression of six established reference genes as measured by qRT-PCR. Ct, cycle threshold. c Correlation between six established reference genes over all non-normalized RNA-seq samples, sorted by transcript abundance. The lowly expressed cysG, idnT, and hcaT are positively correlated (shown in yellow), but negatively correlated with the more abundant ihfB and rrsA. The colour scale bar reflects Pearson’s rho. d Log2-ratio distribution in cross-condition comparisons, shown for RPKM, Upper Quartile (UQ), Trimmed-Mean of M-values (TMM), DESeq2, and moose 2. e Hierarchical clustering based on the Euclidean distance between RNA-seq samples. Matched conditions indicated as blue (0 min), black (30 min), and red (90 min)

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