I have to extract total RNA from E.coli for microarray
experiment. I analyzed my RNA using 2100 Bioanalyzer
and it provides information about rRNA ratio. I did
some search and found that mostly 23s/16s rRNA ratio
for good RNA quality is about 2:1. My results from
Bioanalyzer are vary from 1.8 to 2.6.
My questions are:
1. What rRNA ratio tell me about my RNA?
2. Why they said that the 23s/16s ratio of 2:1 is
good? Why 2:1?
3. Is my RNA in good shape judging from rRNA ratio
that I got?
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In general the 23S rRNA is more labile than the 16S. So the ratio will
decrease as the 23S degrades. The lower the ratio the more degradation has
There are more nucleotides per molecule to bind the dye used in the assay so
the 23S peak should be larger given a 1:1 molecular ratio of rRNA subunits.
I guess the exact figure is dependant on the organism.
Yes. Other things to look for are 23/16S peaks of about the same height and
a relatively flat baseline. Agilent now sell software which gives an RNA
Integrity Number but I am not sure how well validated it is for prokaryotic