I have been asked to prepare some sequencing libraries for a collaborator from pellets of psuedomonas bacteria that were in stationary phase. I isolated RNA and ran it on the agilent 2100 Bioanalyzer with an RNA nano chip. My results were fairly interesting, as there appears to be very little rRNA detected, however there doesn't appear to be any of the usual signs on degradation. For instance, the ribosomal peaks that do appear are very sharp, and there really isn't really much of a slope. I can think of four possibilities, do any of these make sense?
1) As the bacteria were growing in stationary, the rRNA was greatly downregulated as growth slowed.
2) Somehow the RNA extraction enriched for small RNA populations
3) Some small transcript is swamping out the rest of the ribosomal populations
4) The RNA is degraded
What do you guys think?
1) As the bacteria were growing in stationary, the rRNA was greatly downregulated as growth slowed.
2) Somehow the RNA extraction enriched for small RNA populations
3) Some small transcript is swamping out the rest of the ribosomal populations
4) The RNA is degraded
What do you guys think?
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