Advancing the quality control methodology,,,to assess isolated total RNA,,,and generated fragmented cRNA
bioanalyzer and the MOPS gels,
some of them that were failed
using the Agilent software
were passed using gel electrophoresis,
and vice versa.
Some samples that were
passed using the bioanalyzer
and failed on the MOPS gel are
shown in Figures 7 and 8.
Based upon the electropherograms,
the acceptable quality
of the samples is clearly determined,
yet on the MOPS gel
images a ribosomal band is
missing from each.
Just as the MOPS gel is capable
of giving false negatives, it is
also capable of giving false
positives. Some examples of
samples that were passed on
the MOPS gel but failed on the
bioanalyzer are shown in Figures
9 and 10. (Note: Samples
that were passed using the
MOPS gels were failed by QC
measures further along in the
Based upon these observations,
there are clearly more
distinguishable results on the
electropherograms produced using the bioanalyzer then there
are in the MOPS gel images. There
is a lot more room for human and
mechanical error using the MOPS
gels, which may contribute to the
Agilent 2100 bioanalyzer vs MOPS
gels for fragmented cRNA
When analyzing fragmented cRNA,
what is examined is that the sample
has been allowed to heat long
enough and is fully fragmented to
a desirable level. The size of the
fragments can be estimated using
the ladder on the MOPS gel, but
this is not conclusive and determination
of fragmentation is very
subjective due to the poor resolution
of low molecular weight components
(refer to Figures 1-3). The
mRNA Smear Nano assay used
with the bioanalyzer is capable of
showing the desired fragment
length range and percentage of the
total area for each sample. This is
an extremely valuable tool
Source:Page: All 1 2 3 4 5 6 Related biology technology :1
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Eppendorf Phase Lock Gel
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