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Fig. 5 | BMC Genomics

Fig. 5

From: A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures

Fig. 5

Transcription analysis of vps and rbm genes among N16961 phase variants. a Normalized RNA expression profiles based on RNA-seq results for biofilm-related genes. Peaks corresponding to the number of transcripts that mapped to regions containing the vpsI, vpsII, and rbm gene clusters are shown in parallel tracks for each phase variant. N16961 samples are depicted in green, N16961R samples are shown in red, and N16961SD samples are shown in blue. Although our analysis reported similar up-regulated expression values of the genes of all three clusters in the N16961R and N16961SD samples as compared to N16961, some genes of the vpsI cluster fell out of the range of statistical significance in the N16961SD samples (Additional file 10: Table S6). These include the vpsI gene, which encodes a glycosyltransferase, the vpsE and vpsH genes, whose products are predicted to be involved VPS export, and the vpsF and vpsJ genes, which encode proteins of unknown function. The increased P adj values obtained for these genes may be a result of the apparent differences in expression of the vpsI cluster in the SD3 sample versus SD1 and SD2, which can be seen in the figure. b RT-qPCR verification of up-regulation of genes representative of the vpsI, vpsII, and rbm gene clusters in N16961R and N16961SD samples. The graph depicts the log2 fold changes of gene transcripts calculated for each selected gene relative to their transcript abundances in the N16961 sample group at a confidence interval of 95%. All data were normalized respective to the reference gene, gyrA, and the error bars depict the normalized quantity standard error

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