bacterial RNAseq using TruSeq Lib prep

[thiNGS]

Hi all. I am in the process of starting RNAseq from bacterial samples and I am trying to identify the best strategy to do it. Given that bacterial RNA is not poly-adenylated, a random hexamer-based system is essential. Has anyone used the TruSeq stranded library prep kit for bacterial RNA? Or do you have a good kit to recommend? The samples will be run on the MiSeq or NextSeq systems. Any advice to guide me through the magical world of RNAseq will be much appreciated

[huguesparri]

We used the Truseq kit succesfully on Bacteria. 2 things are essential:
- DNAse treatment of your RNA.
- Good depletion efficiency for the ribosomal RNA. Ribozero kit are usually doing well.