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I'm using Life Technologies' MICROBEnrich and MICROBExpress kits in conjunction to deplete prokaryotic/eukaryotic rRNAs and polyadenylated transcripts through capture hybridization. I'm consistently able to deplete the 16S, 18S, and 23S rRNA peaks using the kit's provided control RNA (see the attached TapeStation trace for an example of a successful 18S depletion) but my 28S peaks only shift slightly in their proportion to the rest of the transcripts. For reference, the control RNA is a mixture of rat and E.coli total RNA (10:1 ratio by mass) and the attached trace shows duplicate samples taken through the kit and a negative control consisting of an identical reaction with the control oligos left out -- I have yet to try these on true samples given the problems I've encountered.
Does anyone have any experience with these kits? If so, do you have any recommendations to increase the efficiency of the 28S rRNA depletion? LT technical support has been responsive but I would also like to ask the seqanswers community.
Thank you!
Does anyone have any experience with these kits? If so, do you have any recommendations to increase the efficiency of the 28S rRNA depletion? LT technical support has been responsive but I would also like to ask the seqanswers community.
Thank you!