no detectable RNA after rRNA depletion
Hi all,
I am working with bacterial RNAseq, and like for many others, the discontinuation of Ribo zero made my life a bit more challenging.
I have been testing an alternative from siTOOLS, called riboPOOLS, but so far I haven't been lucky with it. They are using the oligo method with dynabeads, similar to Ribo zero.
My input RNA is around 2-4 µg, within the range that they require. And I follow every step in the protocol, correctly. However, I am having 0 RNA after the depletion. I tried to measure with Quibit HS RNA assay and Bioanalyzer pico chip, and there is nothing left there.
Before depletion, I can see small and mRNAs from the Bioanalyzer results, but they are gone after the depletion.
I heard about very low concentration of mRNA after rRNA depletion, which makes sense due to the high abundance of rRNA, but I am having 0 mRNA or sRNA after the depletion.
I also did a control experiment, where I lowered the concentration of the oligos they suggest, and after that depletion, I had RNA outcome. This convinces me that I am not making a mistake in the protocol.
Has anyone experienced such a thing? Maybe with the Ribo zero before?
Cheers,
Greta
I am working with bacterial RNAseq, and like for many others, the discontinuation of Ribo zero made my life a bit more challenging.
I have been testing an alternative from siTOOLS, called riboPOOLS, but so far I haven't been lucky with it. They are using the oligo method with dynabeads, similar to Ribo zero.
My input RNA is around 2-4 µg, within the range that they require. And I follow every step in the protocol, correctly. However, I am having 0 RNA after the depletion. I tried to measure with Quibit HS RNA assay and Bioanalyzer pico chip, and there is nothing left there.
Before depletion, I can see small and mRNAs from the Bioanalyzer results, but they are gone after the depletion.
I heard about very low concentration of mRNA after rRNA depletion, which makes sense due to the high abundance of rRNA, but I am having 0 mRNA or sRNA after the depletion.
I also did a control experiment, where I lowered the concentration of the oligos they suggest, and after that depletion, I had RNA outcome. This convinces me that I am not making a mistake in the protocol.
Has anyone experienced such a thing? Maybe with the Ribo zero before?
Cheers,
Greta
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