Retapamullin and Chloramphenicol treated mRNA half-life profiling.

mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in cells that were inhibited in translation initiation (retapamullin) or elongation (chloramphenicol) by shutting of transcription with the antibiotic rifampicin, and following mRNA abundance at 1, 2, 4, 8, and 15 minutes post rifampicin. All RNA measurements were performed on cells grown to mid-log in M2G minimal growth medium. Two biological replicates time coursees were collected from independent starter cultures. Overall design: WT NA10000 cells were treated with Chloramphenicol or Retapamullin, then globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq. Total RNA samples were collected just prior to rifampicin addition, and after 1, 2, 4, 8, or 15 minutes incubation with 100ug/mL rifampicin. Each total RNA sample was depleted of rRNA using the ribozero kit (Illumina) for gram negative bacteria, and subjected to total RNA-seq libraries as in (Ingolia et al. Science 2009). tRNA was left in each sample as an internal control for stable RNA.