I am trying to run a RNA gel, (which I had run a very long time ago, and
time tends to erode all information from my chamaeleonic nervous system!),
ergo, here are the details:
I make a mRNA by the mMessage Machine kit from Ambion. The mRNA is capped,
with a poly A tail of about 19 bases. The insert size is ~2kb, and so I
expect a band around 1.9-2.1 kb.
When I regular agarose gel, I see some band ~1kb. I have two other inserts
about the same size, and I do'nt really see much with them.
I tried running a folmaldehyde gel, and the protocol I followed had a tonne
of EtBr in the sample buffer, which ofcourse runs in the opposite direction,
and gave me a large background. I allowed it to run out of the gel.... then
the bands I got were diffuse, and I could'nt really say what size. The
marker was another story: this one from NEB, which did'nt show up at all.
I obviously don't know too much about RNA gels, and if anyone could shed
some light on how to better the technique or interpret results or even
anything on the Ambion message kit, I'd appreciate it much.