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Bacteria transcriptomics RnaSeq - low output
Hi everyone,
we are testing the v2 RnaSeq kit for IonTorrent in order to do some bacteria transcriptomics.
During library preparations all quality values seems good but when we sequence the output is really low: 20/25 Mbp with three samples in a 314 chip with 60% polyclonals. It seems that the one touch/beads enrichment is the problematic step.
Anyone have any suggestion or modified protocol in order to improve the output?
Just another question: Anyone have suggestion for rRNA depletion using genus specific probes? We need to improve rRNA deplation for the bacteria genus we study because universal (E. coli based?) rRNA depletion methos don't work well for us, expecially for 23S.
Thanks for the help!
we are testing the v2 RnaSeq kit for IonTorrent in order to do some bacteria transcriptomics.
During library preparations all quality values seems good but when we sequence the output is really low: 20/25 Mbp with three samples in a 314 chip with 60% polyclonals. It seems that the one touch/beads enrichment is the problematic step.
Anyone have any suggestion or modified protocol in order to improve the output?
Just another question: Anyone have suggestion for rRNA depletion using genus specific probes? We need to improve rRNA deplation for the bacteria genus we study because universal (E. coli based?) rRNA depletion methos don't work well for us, expecially for 23S.
Thanks for the help!