Greetings!
I want to study ribosomal RNA expression and potential processing sites in bacteria. To such effect, I want to perform an RNA-Seq experiment in order to analyze potential rRNA transcripts isoforms and processing sites.
Conventional RNA-Seq experiments are not designed for the analysis of rRNA expression and generally include a RNA depletion step, which reduces rRNA signal. Notice rRNA in bacteria accounts for ~90% of total RNA.
In the context of studying rRNA processing, would the RNA-Seq approach be appropriate? If so, what rRNA treatment would you recommend to study rRNA expression levels and processing?"
Thank you in advance.
Hi Fernando, usually even if there is a step of rRNA removal, you still have a lot of contaminants. Anyway, you might optimize your library preparation just by skipping that step. You should be able to obtain a lot of rRNA.
Hello Michele, in line with what you pointed out, I thought about skipping the rRNA depletion step, so ~90% of my total RNA will be rRNA. In addition, many rRNA depletion kits are unclear about (i) different ribosomal subunits being depleted equally (ii) whether the final rRNA subunit portions are proportional to the original ones.
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