Am reading a study about a bacteria that can resist UV radiation. They were able to do phylogenetic studies on the 16S rRNA. Then, they exposed the cells to gamma radiation and calculated how many survived.
In another study, they completed draft genome sequence of this bacteria. They did gene annotation to try to determine genes related to the UV resistance and other types of environmental stress.
How feasible and/or useful would it be for the next study to try to perform some type of RNA-sequencing on this bacteria to really pinpoint how the genes change in response to say 3 different levels of UV radiation? Several smaller questions:
1) Is RNA-sequencing possible for bacteria? I have only used eukaryotes before for RNA-sequencing. If it is possible, would any R packages help determine "differentially expressed genes". For instance, with eukaryotes, I used DESeq2 to obtain DEGs. What would one use to determine DEGs when bacteria is exposed to different levels of UV radiation?
2) Would methylation studies be of interest for these 3 different levels of UV radiation in a bacteria? What type of R package would be useful for bacterial methylation?
3) How much would such an RNA-sequencing experiment cost? Say I had 3 reps (3 cultures of cells) in each of these 3 UV radiation level groups. I would have 9 samples.
4) How much would such a methylation experiment cost? Say I had 3 reps (3 cultures of cells) in each of these 3 UV radiation level groups. I would have 9 samples.
Even if anyone can answer one of these questions, I would be grateful. I am new to prokaryotes and feeling overwhelmed with trying to compare and contrast with what I know about eukaryotic RNA-sequencing and methylation studies. Thank you many fold to anyone who can kindly share advice/knowledge on this matter.