Has anyone seen Total RNA profiles like this? There is degradation but also some other contaminant. The lab told us that these are from mouse colon and bacterial RNA can be a contaminant. They repeated RNA extraction and got similar profiles. Tissue was frozen on dry ice and wasn't subjected to free-thaw. However, it's clear that these are partially degraded. Could the spikes be due to bacterial RNA contamination? Thank you for your input.
HI Pabalu,
Probability of getting bacterial RNA from mouse colon is too low until or unless there is infection or gut or fecal content is not properly clean from the tissue, during biopsy.
I recommend you to clean your tissue properly in 1XPBS or normal saline, aliquote it into small pieces and store in RNAlater solution in -80. Follow the trizol manual method for RNA extraction with proper safety measurements like RNAase free environment,and store your RNA in RNA storage solution.
you may find this publication useful for your sample prep. It appears to be a known issue.
Article Degradation of intestinal mRNA: A matter of treatment
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