Field of Science

List of RNAseq analyses to do

In case we have money for lots of RNAseq runs, here's a list of every sample that might be useful:

24 samples = 1 run:
Replicates of the samples we've already done:  MIV competence induction at t=0, t=10, t=30 and t=100:
  • 1 x KW20, 
  • 1 x sxy-, 
  • 2 x ∆HI0659, 
  • 2 x ∆HI0660.
Miscellaneous samples (3 replicates of each?):
  • KW20 in late-log (time of max 'spontaneous' competence)
  • KW20 in log phase + hydroxyurea: t=0, t=30? t=60? 
  • HI0659/0660 double mutant, in MIV at t=0 (= log phase) and t=???
  • murE749 mutant in log phase growth and stationary phase
  • Other hypercompetence mutants:  murE750, 751, 752?  in log phase growth
  • mystery hypercompetence mutant RR753 or backcross, in log phase and late-log?
  • KW20 in log phase growth as control (duplicating earlier MIV t=0?)
  • gcvA mutant in MIV?  or in murE749 background in log phase?
  • hfq mutant in MIV?  in log phase too.
  • purR? purH, crp? cya?
  • Cells in MIV + AMP.

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