Fig. 1

Overview of global mRNA decay analysis. a Growth of G. oxydans 621H in the presence of different concentrations of rifampicin as well as the controls methanol and water. The addition of rifampicin or a control is indicated by the arrow. b Formaldehyde agarose gel (1.8%) analysis to inspect the quality of total RNA isolated from G. oxydans cells before and 2, 5, 10, and 15 min after addition of 150 μg/mL of rifampicin. Aliquots of 1 μg of total RNA were loaded. Bands corresponding to the 23S rRNAs (2709 to 2711 nt) and the 16S rRNAs (1478 nt) are indicated as well as the sizes of the RNA fragments present in the RiboRuler Low Range RNA Ladder (M). w/o Rif, without rifampicin. c Schema of the experimental design. RNA isolated at the given time points were mixed with Spike-In RNA mix A or B and used for cDNA synthesis and Cy3 or Cy5 labeling. cDNA synthesized from RNA isolated from cells before addition of rifampicin (t0) and 2, 5, 10, and 15 min after addition of 150 μg/mL rifampicin were pairwise mixed and hybridized on Agilent 4-plex arrays. mRNA half-lives were calculated based on three biological replicates including dye-swap labeling. d Histogram showing the distribution of calculated mRNA half-lives of 2500 genes from G. oxydans where R² was > 0.7 when using all four or the first three sampling times