Hi everybody. I generated RNA samples from Pseudomonas-infected epithelial cells for a dual RNA sequencing. According to the bioanalyzer results, my uninfected controls also contain bacterial RNA.
I would like to confirm this possible contamination by qPCR. Can you suggest a suitable marker gene or other methods to me? If I understood correctly, 16s rRNA would not be specific, since it is also contained in mitochondria.
Thank you.
Hi Sven Cleeves ! If I understand you well your goal is NGS or eucaryotic RNA from cell culture. And you have probable contamination - viral RNA.
On the base on my experience more heterogeneous library is better for subsequent analysis. Bacterial or viral RNA could help. On the other hand viral transcripts may be considered like a source of troubles if you want to analyze specific role of bacterial RNA or cell RNA.
It depends on your experiment design and final goal. May be it is ok for you may be no.
Of course, be sure that your chemistry and instrument could provide you necessary volume of output data, read length, quality etc.
what I heard about is that even the pcr polymerase contains some kind or bacterial DNA/RNA contamination.
Thank you for your replies.
My goal is actually NGS of both eukaryotic and prokaryotic RNA (from infected human cells) in parallel.
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